HEADER HYDROLASE 20-JUN-22 8DEK TITLE THE STRUCTURE OF THE GLYCOPEPTIDASE CATALYTIC DOMAIN INCLUDING THE TITLE 2 LINKER OF AMUC_1438 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NPCBM/NEW2 DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: B, A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AKKERMANSIA MUCINIPHILA; SOURCE 3 ORGANISM_TAXID: 239935; SOURCE 4 GENE: J5W73_07385; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS GLYCOPEPTIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.J.MEDLEY,A.B.BORASTON REVDAT 4 22-MAY-24 8DEK 1 REMARK REVDAT 3 12-OCT-22 8DEK 1 JRNL REVDAT 2 14-SEP-22 8DEK 1 JRNL REVDAT 1 31-AUG-22 8DEK 0 JRNL AUTH B.J.MEDLEY,L.LECLAIRE,N.THOMPSON,K.E.MAHONEY,B.PLUVINAGE, JRNL AUTH 2 M.A.H.PARSON,J.E.BURKE,S.MALAKER,W.WAKARCHUK,A.B.BORASTON JRNL TITL A PREVIOUSLY UNCHARACTERIZED O-GLYCOPEPTIDASE FROM JRNL TITL 2 AKKERMANSIA MUCINIPHILA REQUIRES THE TN-ANTIGEN FOR CLEAVAGE JRNL TITL 3 OF THE PEPTIDE BOND. JRNL REF J.BIOL.CHEM. V. 298 02439 2022 JRNL REFN ESSN 1083-351X JRNL PMID 36049519 JRNL DOI 10.1016/J.JBC.2022.102439 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 36381 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1827 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.9200 - 5.8700 0.96 2780 157 0.1831 0.2038 REMARK 3 2 5.8600 - 4.6600 0.99 2743 149 0.1913 0.2496 REMARK 3 3 4.6600 - 4.0800 0.99 2714 141 0.1861 0.2328 REMARK 3 4 4.0800 - 3.7100 0.98 2691 126 0.2114 0.2552 REMARK 3 5 3.7100 - 3.4400 0.99 2634 151 0.2180 0.2525 REMARK 3 6 3.4400 - 3.2400 0.99 2662 150 0.2512 0.3025 REMARK 3 7 3.2400 - 3.0800 0.99 2676 143 0.2825 0.3659 REMARK 3 8 3.0800 - 2.9400 0.99 2630 155 0.2983 0.3780 REMARK 3 9 2.9400 - 2.8300 0.99 2655 144 0.2984 0.3818 REMARK 3 10 2.8300 - 2.7300 0.99 2650 134 0.3114 0.4058 REMARK 3 11 2.7300 - 2.6500 0.98 2653 116 0.2976 0.3473 REMARK 3 12 2.6500 - 2.5700 0.97 2582 152 0.2954 0.3764 REMARK 3 13 2.5700 - 2.5000 0.91 2484 109 0.2890 0.3832 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.427 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 6727 REMARK 3 ANGLE : 0.449 9141 REMARK 3 CHIRALITY : 0.040 977 REMARK 3 PLANARITY : 0.004 1200 REMARK 3 DIHEDRAL : 3.866 962 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 19 through 23 or REMARK 3 (resid 24 and (name N or name CA or name REMARK 3 C or name O or name CB or name CG )) or REMARK 3 resid 25 through 33 or (resid 34 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB or name CG or name CD or name NE ) REMARK 3 ) or resid 35 through 43 or (resid 44 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 45 through 54 or REMARK 3 (resid 55 and (name N or name CA or name REMARK 3 C or name O or name CB or name CG or name REMARK 3 CD )) or resid 56 through 72 or (resid 73 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB or name CG or name CD2)) or REMARK 3 (resid 74 and (name N or name CA or name REMARK 3 C or name O or name CB or name CG )) or REMARK 3 resid 75 through 123 or (resid 124 REMARK 3 through 125 and (name N or name CA or REMARK 3 name C or name O or name CB or name CG or REMARK 3 name CD )) or resid 126 through 131 or REMARK 3 (resid 132 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 133 REMARK 3 through 139 or (resid 140 through 142 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 143 through 154 or REMARK 3 (resid 155 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 156 REMARK 3 through 163 or (resid 164 and (name N or REMARK 3 name CA or name C or name O or name CB or REMARK 3 name CG )) or resid 165 through 198 or REMARK 3 (resid 199 and (name N or name CA or name REMARK 3 C or name O )) or resid 200 through 315 REMARK 3 or (resid 316 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 317 through 341 or (resid 342 and (name N REMARK 3 or name CA or name C )) or resid 343 REMARK 3 through 346 or (resid 347 and (name N or REMARK 3 name CA or name C or name O or name CB or REMARK 3 name CG or name OD1)) or resid 348 REMARK 3 through 359 or (resid 360 and (name N or REMARK 3 name CA or name C or name O or name CB or REMARK 3 name CG )) or resid 361 through 402 or REMARK 3 (resid 403 and (name N or name CA or name REMARK 3 C or name O or name CB or name CG or name REMARK 3 CD )) or resid 404 through 437 or (resid REMARK 3 438 and (name N or name CA or name C or REMARK 3 name O or name CB )) or resid 439 through REMARK 3 440 or (resid 441 and (name N or name CA REMARK 3 or name C or name O or name CB )) or REMARK 3 resid 442 through 445 or (resid 446 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 447 through 458)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 19 through 50 or REMARK 3 (resid 51 and (name N or name CA or name REMARK 3 C or name O or name CB or name CG or name REMARK 3 CD )) or resid 52 through 67 or (resid 68 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB )) or resid 69 through 111 REMARK 3 or (resid 112 and (name N or name CA or REMARK 3 name C or name O or name CB or name CG )) REMARK 3 or resid 113 or (resid 114 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 115 through 122 or (resid 123 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB or name CG or name OD1)) or REMARK 3 resid 124 through 130 or (resid 131 REMARK 3 through 132 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 133 through 143 or (resid 144 and (name N REMARK 3 or name CA or name C or name O or name CB REMARK 3 )) or resid 145 through 148 or (resid 149 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB )) or resid 150 through 152 REMARK 3 or (resid 153 and (name N or name CA or REMARK 3 name C or name O or name CB or name CG1)) REMARK 3 or resid 154 through 189 or (resid 190 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB or name CG or name CD1)) or REMARK 3 resid 191 through 195 or (resid 196 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 197 through 201 or REMARK 3 (resid 202 through 204 and (name N or REMARK 3 name CA or name C or name O )) or resid REMARK 3 205 through 241 or (resid 242 and (name N REMARK 3 or name CA or name C or name O or name CB REMARK 3 or name CG or name OD2)) or resid 243 REMARK 3 through 261 or (resid 262 through 263 and REMARK 3 (name N or name CA or name C or name O )) REMARK 3 or resid 264 through 294 or (resid 295 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB )) or resid 296 through 310 REMARK 3 or (resid 311 through 312 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or (resid 313 and (name N or name CA or REMARK 3 name C or name O or name CB or name CG1 REMARK 3 or name CG2)) or resid 314 through 321 or REMARK 3 (resid 322 and (name N or name CA or name REMARK 3 C or name O or name CB or name CG or name REMARK 3 CD or name CE )) or resid 323 through 355 REMARK 3 or (resid 356 and (name N or name CA or REMARK 3 name C or name O or name CB or name CG or REMARK 3 name OD2)) or (resid 357 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or (resid 358 and (name N or name CA or REMARK 3 name C or name O or name CB or name CG )) REMARK 3 or resid 359 through 392 or (resid 393 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB or name CG or name CD2)) or REMARK 3 resid 394 through 408 or (resid 409 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB or name CG or name CD )) or resid REMARK 3 410 through 425 or (resid 426 and (name N REMARK 3 or name CA or name C or name O or name CB REMARK 3 )) or resid 427 through 429 or (resid 430 REMARK 3 through 431 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 432 through 433 or (resid 434 and (name N REMARK 3 or name CA or name C or name O or name CB REMARK 3 or name CG or name CD or name OE2)) or REMARK 3 resid 435 or (resid 436 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 437 through 458)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8DEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1000266508. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-002 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54187 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36634 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M (NH4)2PO4, 20% (W/V) PEG3350, AND REMARK 280 0,1M BICINE, PH 9.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 35.61650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 80.83700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.73550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 80.83700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.61650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.73550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A 18 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG B 18 O CG CD NE CZ NH1 NH2 REMARK 470 GLU B 21 CG CD OE1 OE2 REMARK 470 ARG B 24 CD NE CZ NH1 NH2 REMARK 470 ARG B 34 CZ NH1 NH2 REMARK 470 LYS B 44 CG CD CE NZ REMARK 470 ARG B 51 NH1 REMARK 470 LYS B 55 CE NZ REMARK 470 LYS B 59 CE NZ REMARK 470 LYS B 68 NZ REMARK 470 LEU B 73 CD1 REMARK 470 GLU B 74 CD OE1 OE2 REMARK 470 GLU B 78 CG CD OE1 OE2 REMARK 470 GLU B 111 CG CD OE1 OE2 REMARK 470 ARG B 112 CZ NH1 NH2 REMARK 470 LYS B 124 CE NZ REMARK 470 MET B 126 CE REMARK 470 GLN B 132 CG CD OE1 NE2 REMARK 470 VAL B 137 CG1 CG2 REMARK 470 GLU B 140 CG CD OE1 OE2 REMARK 470 LYS B 149 CD CE NZ REMARK 470 LYS B 155 CG CD CE NZ REMARK 470 LEU B 164 CD1 CD2 REMARK 470 GLU B 188 CG CD OE1 OE2 REMARK 470 GLU B 199 CB CG CD OE1 OE2 REMARK 470 GLN B 202 CD OE1 NE2 REMARK 470 ARG B 210 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 264 CD CE NZ REMARK 470 GLU B 288 CG CD OE1 OE2 REMARK 470 ARG B 297 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 316 CG CD CE NZ REMARK 470 GLY B 342 O REMARK 470 ASP B 347 OD2 REMARK 470 GLU B 357 OE1 REMARK 470 LYS B 358 NZ REMARK 470 GLU B 360 CD OE1 OE2 REMARK 470 LYS B 371 CG CD CE NZ REMARK 470 ARG B 400 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 403 CE NZ REMARK 470 ARG B 438 CG CD NE CZ NH1 NH2 REMARK 470 SER B 441 OG REMARK 470 LYS B 446 CG CD CE NZ REMARK 470 ARG B 458 CZ NH1 NH2 REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 LYS A 44 CE NZ REMARK 470 ARG A 51 NE CZ NH1 NH2 REMARK 470 LYS A 59 CE NZ REMARK 470 LYS A 68 CG CD CE NZ REMARK 470 GLU A 78 CG CD OE1 OE2 REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 ARG A 112 CD NE CZ NH1 NH2 REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 ASP A 123 OD2 REMARK 470 MET A 126 CE REMARK 470 VAL A 131 CG1 CG2 REMARK 470 GLN A 132 CD OE1 NE2 REMARK 470 VAL A 137 CG1 CG2 REMARK 470 LYS A 144 CG CD CE NZ REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 ILE A 153 CG2 CD1 REMARK 470 LYS A 155 CE NZ REMARK 470 GLU A 188 CG CD OE1 OE2 REMARK 470 LEU A 190 CD2 REMARK 470 LEU A 196 CG CD1 CD2 REMARK 470 GLU A 199 CG CD OE1 OE2 REMARK 470 GLN A 202 CB CG CD OE1 NE2 REMARK 470 ARG A 210 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 242 OD1 REMARK 470 GLU A 262 CB CG CD OE1 OE2 REMARK 470 LYS A 264 CD CE NZ REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 PHE A 295 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 297 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 311 CG CD OE1 OE2 REMARK 470 ILE A 313 CD1 REMARK 470 LYS A 316 CD CE NZ REMARK 470 LYS A 322 NZ REMARK 470 ASP A 356 OD1 REMARK 470 GLU A 357 CG CD OE1 OE2 REMARK 470 LYS A 358 CD CE NZ REMARK 470 LYS A 371 CG CD CE NZ REMARK 470 LEU A 393 CD1 REMARK 470 ARG A 400 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 403 NZ REMARK 470 GLN A 409 OE1 NE2 REMARK 470 GLU A 426 CG CD OE1 OE2 REMARK 470 LYS A 430 CG CD CE NZ REMARK 470 GLU A 434 OE1 REMARK 470 GLU A 436 CG CD OE1 OE2 REMARK 470 ARG A 438 CZ NH1 NH2 REMARK 470 LYS A 446 CE NZ REMARK 470 ARG A 458 CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO B 102 67.43 -68.04 REMARK 500 VAL B 168 -40.70 -130.35 REMARK 500 PHE B 176 -158.24 -145.75 REMARK 500 SER B 386 -10.12 81.26 REMARK 500 PRO A 102 66.52 -68.55 REMARK 500 VAL A 168 -40.47 -130.48 REMARK 500 PHE A 176 -158.24 -145.89 REMARK 500 GLN A 202 141.03 79.92 REMARK 500 SER A 386 -9.79 81.35 REMARK 500 PHE A 413 17.12 54.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 223 NE2 REMARK 620 2 HIS B 227 NE2 76.2 REMARK 620 3 HIS B 233 NE2 80.0 82.7 REMARK 620 4 HOH B 621 O 162.7 93.0 112.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 223 NE2 REMARK 620 2 HIS A 227 NE2 72.6 REMARK 620 3 HIS A 233 NE2 82.5 80.3 REMARK 620 4 HOH A 627 O 110.1 100.4 167.1 REMARK 620 N 1 2 3 DBREF1 8DEK B 19 458 UNP A0A8F1DJZ3_9BACT DBREF2 8DEK B A0A8F1DJZ3 42 481 DBREF1 8DEK A 19 458 UNP A0A8F1DJZ3_9BACT DBREF2 8DEK A A0A8F1DJZ3 42 481 SEQADV 8DEK ARG B 18 UNP A0A8F1DJZ EXPRESSION TAG SEQADV 8DEK ARG A 18 UNP A0A8F1DJZ EXPRESSION TAG SEQRES 1 B 441 ARG GLY ALA GLU PHE THR ARG LEU PRO VAL SER TRP THR SEQRES 2 B 441 VAL ASN PRO ARG ASP ALA ALA ASN ALA ARG ALA ALA TRP SEQRES 3 B 441 LYS THR LEU SER ALA TYR HIS ARG GLY LYS PRO LYS SER SEQRES 4 B 441 SER ARG LYS LEU HIS VAL VAL TYR VAL THR PHE LYS ASP SEQRES 5 B 441 ARG PRO ALA LEU GLU GLY TYR ARG GLU ARG TYR ASP HIS SEQRES 6 B 441 ILE LEU LYS ASN ILE GLN ALA TYR TYR ALA ASP GLN MET SEQRES 7 B 441 GLN ALA ASN GLY PHE PRO PRO LEU THR PHE GLN LEU ASP SEQRES 8 B 441 LEU ASP GLU ARG GLY LYS LEU VAL ILE HIS ASP ALA TYR SEQRES 9 B 441 VAL ASP LYS PRO MET SER GLU MET SER VAL GLN SER SER SEQRES 10 B 441 GLY PRO VAL SER ARG GLU ALA ALA ARG LYS VAL LEU ALA SEQRES 11 B 441 SER LYS GLY ILE ASP ILE GLU LYS GLU HIS VAL LEU VAL SEQRES 12 B 441 VAL CYS GLN LEU PRO ASP GLY VAL GLY PRO TYR TYR GLY SEQRES 13 B 441 GLY GLY PHE SER HIS GLN GLY THR GLY TRP THR CYS ASP SEQRES 14 B 441 GLN GLU GLY LEU ASP PRO ALA SER PHE LEU ASP THR GLU SEQRES 15 B 441 MET MET GLN GLY GLY ARG PHE LYS VAL THR ARG GLY LYS SEQRES 16 B 441 ASN ALA THR ILE TYR ILE GLY GLY THR ALA HIS GLU LEU SEQRES 17 B 441 GLY HIS SER PHE GLY LEU PRO HIS THR GLY ASP GLY TRP SEQRES 18 B 441 ASN TYR PRO ASP ALA GLY ALA SER LEU MET GLY HIS GLY SEQRES 19 B 441 ASN SER THR TYR GLY ASP GLU LEU ARG HIS GLU GLY LYS SEQRES 20 B 441 GLY ALA TYR LEU ALA PRO THR ASP ALA LEU LYS LEU ALA SEQRES 21 B 441 SER VAL PRO LEU PHE ASN GLY VAL GLU THR GLU LEU PRO SEQRES 22 B 441 ALA ASP ALA SER PHE GLY ARG MET LEU GLY LYS TYR VAL SEQRES 23 B 441 PRO GLY SER PHE GLU ARG LEU GLU ALA ILE PRO VAL LYS SEQRES 24 B 441 ASP GLY LEU ARG LEU LYS GLY ARG VAL HIS LEU THR ARG SEQRES 25 B 441 PRO ALA TYR GLY ILE VAL ALA HIS LEU ASP PRO PRO GLY SEQRES 26 B 441 GLY SER ASP TYR ASP SER ASN ALA VAL GLY ALA SER LEU SEQRES 27 B 441 ASP GLU LYS GLY GLU PHE ASP LEU THR ILE CYS ARG PRO SEQRES 28 B 441 GLY TYR LYS GLY GLY PHE ILE GLU MET ARG VAL ALA VAL SEQRES 29 B 441 LEU ASN CYS ASP SER THR ARG SER MET ILE THR LEU PRO SEQRES 30 B 441 VAL TRP MET ASP ALA ARG GLY THR LYS ALA PRO SER LEU SEQRES 31 B 441 ALA GLN ILE VAL TYR PHE GLY ASP VAL GLN ASN LEU TRP SEQRES 32 B 441 ILE ARG GLY ARG THR GLU GLU ALA ARG LYS ALA LEU ALA SEQRES 33 B 441 GLU VAL GLU ARG ARG HIS GLY SER ARG SER GLU VAL LYS SEQRES 34 B 441 GLU TRP LEU PRO VAL TRP LYS ARG ALA LEU GLY ARG SEQRES 1 A 441 ARG GLY ALA GLU PHE THR ARG LEU PRO VAL SER TRP THR SEQRES 2 A 441 VAL ASN PRO ARG ASP ALA ALA ASN ALA ARG ALA ALA TRP SEQRES 3 A 441 LYS THR LEU SER ALA TYR HIS ARG GLY LYS PRO LYS SER SEQRES 4 A 441 SER ARG LYS LEU HIS VAL VAL TYR VAL THR PHE LYS ASP SEQRES 5 A 441 ARG PRO ALA LEU GLU GLY TYR ARG GLU ARG TYR ASP HIS SEQRES 6 A 441 ILE LEU LYS ASN ILE GLN ALA TYR TYR ALA ASP GLN MET SEQRES 7 A 441 GLN ALA ASN GLY PHE PRO PRO LEU THR PHE GLN LEU ASP SEQRES 8 A 441 LEU ASP GLU ARG GLY LYS LEU VAL ILE HIS ASP ALA TYR SEQRES 9 A 441 VAL ASP LYS PRO MET SER GLU MET SER VAL GLN SER SER SEQRES 10 A 441 GLY PRO VAL SER ARG GLU ALA ALA ARG LYS VAL LEU ALA SEQRES 11 A 441 SER LYS GLY ILE ASP ILE GLU LYS GLU HIS VAL LEU VAL SEQRES 12 A 441 VAL CYS GLN LEU PRO ASP GLY VAL GLY PRO TYR TYR GLY SEQRES 13 A 441 GLY GLY PHE SER HIS GLN GLY THR GLY TRP THR CYS ASP SEQRES 14 A 441 GLN GLU GLY LEU ASP PRO ALA SER PHE LEU ASP THR GLU SEQRES 15 A 441 MET MET GLN GLY GLY ARG PHE LYS VAL THR ARG GLY LYS SEQRES 16 A 441 ASN ALA THR ILE TYR ILE GLY GLY THR ALA HIS GLU LEU SEQRES 17 A 441 GLY HIS SER PHE GLY LEU PRO HIS THR GLY ASP GLY TRP SEQRES 18 A 441 ASN TYR PRO ASP ALA GLY ALA SER LEU MET GLY HIS GLY SEQRES 19 A 441 ASN SER THR TYR GLY ASP GLU LEU ARG HIS GLU GLY LYS SEQRES 20 A 441 GLY ALA TYR LEU ALA PRO THR ASP ALA LEU LYS LEU ALA SEQRES 21 A 441 SER VAL PRO LEU PHE ASN GLY VAL GLU THR GLU LEU PRO SEQRES 22 A 441 ALA ASP ALA SER PHE GLY ARG MET LEU GLY LYS TYR VAL SEQRES 23 A 441 PRO GLY SER PHE GLU ARG LEU GLU ALA ILE PRO VAL LYS SEQRES 24 A 441 ASP GLY LEU ARG LEU LYS GLY ARG VAL HIS LEU THR ARG SEQRES 25 A 441 PRO ALA TYR GLY ILE VAL ALA HIS LEU ASP PRO PRO GLY SEQRES 26 A 441 GLY SER ASP TYR ASP SER ASN ALA VAL GLY ALA SER LEU SEQRES 27 A 441 ASP GLU LYS GLY GLU PHE ASP LEU THR ILE CYS ARG PRO SEQRES 28 A 441 GLY TYR LYS GLY GLY PHE ILE GLU MET ARG VAL ALA VAL SEQRES 29 A 441 LEU ASN CYS ASP SER THR ARG SER MET ILE THR LEU PRO SEQRES 30 A 441 VAL TRP MET ASP ALA ARG GLY THR LYS ALA PRO SER LEU SEQRES 31 A 441 ALA GLN ILE VAL TYR PHE GLY ASP VAL GLN ASN LEU TRP SEQRES 32 A 441 ILE ARG GLY ARG THR GLU GLU ALA ARG LYS ALA LEU ALA SEQRES 33 A 441 GLU VAL GLU ARG ARG HIS GLY SER ARG SER GLU VAL LYS SEQRES 34 A 441 GLU TRP LEU PRO VAL TRP LYS ARG ALA LEU GLY ARG HET ZN B 501 1 HET NA B 502 1 HET EDO A 501 4 HET ZN A 502 1 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 NA NA 1+ FORMUL 5 EDO C2 H6 O2 FORMUL 7 HOH *60(H2 O) HELIX 1 AA1 GLY B 19 THR B 23 5 5 HELIX 2 AA2 ASN B 32 ARG B 51 1 20 HELIX 3 AA3 GLY B 75 ASN B 98 1 24 HELIX 4 AA4 PRO B 125 MET B 129 5 5 HELIX 5 AA5 SER B 130 LYS B 149 1 20 HELIX 6 AA6 ASP B 152 LYS B 155 5 4 HELIX 7 AA7 ASP B 191 ASP B 197 5 7 HELIX 8 AA8 THR B 209 PHE B 229 1 21 HELIX 9 AA9 HIS B 250 THR B 254 5 5 HELIX 10 AB1 GLY B 256 HIS B 261 5 6 HELIX 11 AB2 ALA B 269 ALA B 277 1 9 HELIX 12 AB3 VAL B 279 GLY B 284 1 6 HELIX 13 AB4 SER B 344 SER B 348 5 5 HELIX 14 AB5 LYS B 403 TYR B 412 1 10 HELIX 15 AB6 PHE B 413 ILE B 421 1 9 HELIX 16 AB7 ARG B 424 GLY B 440 1 17 HELIX 17 AB8 ARG B 442 GLU B 447 1 6 HELIX 18 AB9 GLU B 447 LEU B 456 1 10 HELIX 19 AC1 GLY B 457 ARG B 458 5 2 HELIX 20 AC2 GLY A 19 THR A 23 5 5 HELIX 21 AC3 ASN A 32 ARG A 51 1 20 HELIX 22 AC4 GLY A 75 ASN A 98 1 24 HELIX 23 AC5 PRO A 125 MET A 129 5 5 HELIX 24 AC6 SER A 130 LYS A 149 1 20 HELIX 25 AC7 ASP A 152 LYS A 155 5 4 HELIX 26 AC8 ASP A 191 ASP A 197 5 7 HELIX 27 AC9 THR A 209 PHE A 229 1 21 HELIX 28 AD1 HIS A 250 THR A 254 5 5 HELIX 29 AD2 GLY A 256 HIS A 261 5 6 HELIX 30 AD3 ALA A 269 ALA A 277 1 9 HELIX 31 AD4 VAL A 279 GLY A 284 1 6 HELIX 32 AD5 SER A 344 SER A 348 5 5 HELIX 33 AD6 LYS A 403 TYR A 412 1 10 HELIX 34 AD7 PHE A 413 ILE A 421 1 9 HELIX 35 AD8 ARG A 424 GLY A 440 1 17 HELIX 36 AD9 ARG A 442 GLU A 447 1 6 HELIX 37 AE1 GLU A 447 LEU A 456 1 10 SHEET 1 AA1 5 ILE B 117 VAL B 122 0 SHEET 2 AA1 5 LEU B 60 PHE B 67 1 N TYR B 64 O ALA B 120 SHEET 3 AA1 5 HIS B 157 CYS B 162 1 O VAL B 161 N VAL B 65 SHEET 4 AA1 5 GLY B 180 CYS B 185 1 O GLY B 182 N VAL B 160 SHEET 5 AA1 5 TYR B 172 GLY B 175 -1 N TYR B 172 O TRP B 183 SHEET 1 AA2 2 ALA B 245 SER B 246 0 SHEET 2 AA2 2 ALA B 266 TYR B 267 1 O TYR B 267 N ALA B 245 SHEET 1 AA3 2 SER B 294 PHE B 295 0 SHEET 2 AA3 2 LYS B 301 TYR B 302 -1 O TYR B 302 N SER B 294 SHEET 1 AA4 3 PHE B 307 VAL B 315 0 SHEET 2 AA4 3 GLY B 318 VAL B 325 -1 O ARG B 320 N ILE B 313 SHEET 3 AA4 3 GLU B 360 CYS B 366 -1 O ILE B 365 N LEU B 319 SHEET 1 AA5 4 ASN B 349 ALA B 353 0 SHEET 2 AA5 4 ALA B 331 ASP B 339 -1 N ALA B 336 O VAL B 351 SHEET 3 AA5 4 PHE B 374 ASN B 383 -1 O ARG B 378 N HIS B 337 SHEET 4 AA5 4 ARG B 388 TRP B 396 -1 O LEU B 393 N MET B 377 SHEET 1 AA6 5 ILE A 117 VAL A 122 0 SHEET 2 AA6 5 LEU A 60 PHE A 67 1 N TYR A 64 O ALA A 120 SHEET 3 AA6 5 HIS A 157 CYS A 162 1 O VAL A 161 N VAL A 65 SHEET 4 AA6 5 GLY A 180 CYS A 185 1 O GLY A 182 N VAL A 160 SHEET 5 AA6 5 GLY A 173 GLY A 175 -1 N GLY A 174 O THR A 181 SHEET 1 AA7 2 ALA A 245 SER A 246 0 SHEET 2 AA7 2 ALA A 266 TYR A 267 1 O TYR A 267 N ALA A 245 SHEET 1 AA8 2 SER A 294 PHE A 295 0 SHEET 2 AA8 2 LYS A 301 TYR A 302 -1 O TYR A 302 N SER A 294 SHEET 1 AA9 3 PHE A 307 VAL A 315 0 SHEET 2 AA9 3 GLY A 318 VAL A 325 -1 O ARG A 320 N ILE A 313 SHEET 3 AA9 3 GLU A 360 CYS A 366 -1 O ILE A 365 N LEU A 319 SHEET 1 AB1 4 ASN A 349 SER A 354 0 SHEET 2 AB1 4 ALA A 331 ASP A 339 -1 N ALA A 336 O VAL A 351 SHEET 3 AB1 4 PHE A 374 ASN A 383 -1 O ALA A 380 N VAL A 335 SHEET 4 AB1 4 ARG A 388 TRP A 396 -1 O LEU A 393 N MET A 377 LINK NE2 HIS B 223 ZN ZN B 501 1555 1555 2.30 LINK NE2 HIS B 227 ZN ZN B 501 1555 1555 2.30 LINK NE2 HIS B 233 ZN ZN B 501 1555 1555 2.29 LINK ZN ZN B 501 O HOH B 621 1555 1555 2.61 LINK NE2 HIS A 223 ZN ZN A 502 1555 1555 2.30 LINK NE2 HIS A 227 ZN ZN A 502 1555 1555 2.31 LINK NE2 HIS A 233 ZN ZN A 502 1555 1555 2.29 LINK ZN ZN A 502 O HOH A 627 1555 1555 2.57 CRYST1 71.233 91.471 161.674 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014038 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006185 0.00000 MTRIX1 1 -0.953824 0.002716 0.300355 29.14602 1 MTRIX2 1 -0.002173 -0.999995 0.002143 39.28967 1 MTRIX3 1 0.300359 0.001391 0.953825 -3.93851 1