HEADER DNA BINDING PROTEIN 22-APR-24 8Z8Y TITLE CRYSTAL STRUCTURE OF CRTAGO/CRTTIR-APAZ COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIWI DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TIR DOMAIN-CONTAINING PROTEIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOFLAVIFILUM THERMOPHILUM; SOURCE 3 ORGANISM_TAXID: 1393122; SOURCE 4 GENE: SAMN05660895_1671; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: THERMOFLAVIFILUM THERMOPHILUM; SOURCE 9 ORGANISM_TAXID: 1393122; SOURCE 10 GENE: SAMN05660895_1670; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NADASE, DNA, COMPLEX, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.HU,J.CHEN,L.LIU REVDAT 1 12-MAR-25 8Z8Y 0 JRNL AUTH R.HU,C.GUO,X.LIU,Y.LIN,Z.YANG,Z.LI,Y.YANG,E.MA,Y.LI,J.CHEN, JRNL AUTH 2 L.LIU JRNL TITL STRUCTURAL BASIS OF SSDNA-GUIDED NADASE ACTIVATION OF JRNL TITL 2 PROKARYOTIC SPARTA SYSTEM. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 39997222 JRNL DOI 10.1093/NAR/GKAF110 REMARK 2 REMARK 2 RESOLUTION. 3.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 3.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 36416 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.276 REMARK 3 R VALUE (WORKING SET) : 0.274 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1867 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 40.6100 - 7.4600 0.99 2860 155 0.2102 0.2087 REMARK 3 2 7.4600 - 5.9300 1.00 2732 146 0.2655 0.2625 REMARK 3 3 5.9300 - 5.1800 1.00 2678 156 0.2720 0.3117 REMARK 3 4 5.1800 - 4.7100 1.00 2670 129 0.2615 0.3132 REMARK 3 5 4.7100 - 4.3700 1.00 2638 158 0.2690 0.2779 REMARK 3 6 4.3700 - 4.1100 1.00 2676 119 0.2783 0.3233 REMARK 3 7 4.1100 - 3.9100 1.00 2627 139 0.3260 0.4083 REMARK 3 8 3.9100 - 3.7400 1.00 2622 140 0.3317 0.3555 REMARK 3 9 3.7400 - 3.5900 1.00 2641 140 0.3496 0.4146 REMARK 3 10 3.5900 - 3.4700 1.00 2564 173 0.3520 0.3711 REMARK 3 11 3.4700 - 3.3600 1.00 2612 134 0.3772 0.4358 REMARK 3 12 3.3600 - 3.2700 1.00 2652 113 0.3913 0.4368 REMARK 3 13 3.2700 - 3.1800 1.00 2577 165 0.4257 0.4666 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) : 0.611 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 117.8 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 113.6 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 : 0.013 7951 REMARK 3 ANGLE : 1.646 10753 REMARK 3 CHIRALITY : 0.080 1159 REMARK 3 PLANARITY : 0.008 1371 REMARK 3 DIHEDRAL : 25.583 2971 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8Z8Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 26-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300047213. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98322 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 7.21 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 1.17.1_3660 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36475 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.180 REMARK 200 RESOLUTION RANGE LOW (A) : 40.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 39.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 40.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHENIX 1.17.1_3660 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, 0.1 M TRIS, PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 122.90000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.45000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 92.17500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.72500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 153.62500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 122.90000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 61.45000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 30.72500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 92.17500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 153.62500 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: 7190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLU B 447 REMARK 465 ASP B 448 REMARK 465 ILE B 449 REMARK 465 GLU B 450 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 LYS A 314 CG CD CE NZ REMARK 470 LYS A 351 CG CD CE NZ REMARK 470 HIS B 9 CG ND1 CD2 CE1 NE2 REMARK 470 LEU B 103 CG CD1 CD2 REMARK 470 LEU B 159 CG CD1 CD2 REMARK 470 HIS B 160 CG ND1 CD2 CE1 NE2 REMARK 470 ASP B 161 CG OD1 OD2 REMARK 470 LYS B 162 CG CD CE NZ REMARK 470 ILE B 165 CG1 CG2 CD1 REMARK 470 GLU B 166 CG CD OE1 OE2 REMARK 470 LYS B 167 CG CD CE NZ REMARK 470 GLU B 168 CG CD OE1 OE2 REMARK 470 LYS B 366 CG CD CE NZ REMARK 470 LYS B 409 CG CD CE NZ REMARK 470 PHE B 411 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU B 424 CG CD1 CD2 REMARK 470 LEU B 430 CG CD1 CD2 REMARK 470 ILE B 433 CG1 CG2 CD1 REMARK 470 ASN B 435 CG OD1 ND2 REMARK 470 PHE B 436 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU B 443 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP B 442 MG MG B 501 1.53 REMARK 500 O ASP B 14 OG1 THR B 18 1.53 REMARK 500 O ASP B 199 OG1 THR B 202 1.59 REMARK 500 OE1 GLU A 145 NH2 ARG A 225 1.63 REMARK 500 NE2 GLN A 302 O THR A 479 1.65 REMARK 500 NE2 HIS A 207 OD1 ASP B 442 1.66 REMARK 500 O VAL B 80 CG2 VAL B 84 1.70 REMARK 500 CE1 PHE B 60 CD1 LEU B 78 1.71 REMARK 500 CG2 THR B 82 OE2 GLU B 111 1.72 REMARK 500 O GLY B 27 N ASP B 146 1.74 REMARK 500 OH TYR A 262 OD1 ASP A 309 1.74 REMARK 500 OG1 THR A 228 OE1 GLU B 441 1.75 REMARK 500 O LEU B 28 CA PRO B 145 1.77 REMARK 500 O VAL B 80 N VAL B 84 1.84 REMARK 500 O ARG A 152 OG SER A 155 1.85 REMARK 500 O ASP A 123 OG1 THR A 127 1.85 REMARK 500 CA ASN B 367 OE2 GLU B 427 1.86 REMARK 500 O PHE A 183 ND2 ASN A 187 1.88 REMARK 500 OE1 GLN A 18 ND2 ASN B 151 1.88 REMARK 500 ND2 ASN B 258 OE1 GLN B 262 1.88 REMARK 500 OD1 ASN A 307 N ASP A 309 1.89 REMARK 500 NE ARG B 193 OG1 THR B 232 1.89 REMARK 500 C VAL B 80 CG2 VAL B 84 1.93 REMARK 500 CD ARG B 283 OE1 GLU B 296 1.94 REMARK 500 CD1 LEU A 271 O ASP A 306 1.94 REMARK 500 O ALA B 81 N LYS B 85 1.95 REMARK 500 OD1 ASP B 387 N ALA B 390 1.96 REMARK 500 O LYS B 4 N CYS B 58 1.97 REMARK 500 OE1 GLN A 18 CG ASN B 151 1.97 REMARK 500 NZ LYS A 347 OH TYR A 353 1.97 REMARK 500 OG1 THR B 253 N ILE B 256 1.98 REMARK 500 OE2 GLU A 9 OH TYR A 472 1.98 REMARK 500 OD1 ASP B 346 N ILE B 348 1.98 REMARK 500 CD1 ILE B 208 CD2 LEU B 268 1.98 REMARK 500 NZ LYS A 263 O ILE A 507 1.98 REMARK 500 O ILE B 53 OG1 THR B 57 1.99 REMARK 500 OH TYR B 210 CD1 ILE B 256 1.99 REMARK 500 O ALA A 253 OG SER A 257 2.00 REMARK 500 CZ PHE B 60 CD1 LEU B 78 2.01 REMARK 500 NH1 ARG A 72 OE2 GLU B 426 2.01 REMARK 500 CE2 TYR A 148 OG1 THR B 440 2.01 REMARK 500 OD1 ASP B 100 N ASN B 102 2.01 REMARK 500 CG2 ILE B 178 CE2 PHE B 181 2.03 REMARK 500 OE2 GLU A 344 OH TYR A 353 2.03 REMARK 500 NZ LYS A 211 O ILE A 507 2.03 REMARK 500 OE1 GLN A 18 OD1 ASN B 151 2.04 REMARK 500 OE1 GLU A 436 NH2 ARG B 361 2.05 REMARK 500 OD2 ASP B 119 NZ LYS B 121 2.07 REMARK 500 OE1 GLU A 9 NZ LYS A 464 2.07 REMARK 500 O LYS B 366 OE2 GLU B 427 2.07 REMARK 500 REMARK 500 THIS ENTRY HAS 68 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O PHE A 93 NH1 ARG B 114 12544 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 299 CB CYS A 299 SG -0.118 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 180 C - N - CD ANGL. DEV. = -12.9 DEGREES REMARK 500 PRO A 241 C - N - CD ANGL. DEV. = 12.8 DEGREES REMARK 500 PRO A 268 C - N - CD ANGL. DEV. = 12.7 DEGREES REMARK 500 PRO A 393 C - N - CD ANGL. DEV. = 13.1 DEGREES REMARK 500 LEU A 490 CA - CB - CG ANGL. DEV. = -15.0 DEGREES REMARK 500 PRO B 12 C - N - CD ANGL. DEV. = 17.7 DEGREES REMARK 500 LEU B 408 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 16 3.93 83.40 REMARK 500 PRO A 73 130.72 -33.43 REMARK 500 ASN A 90 77.20 -118.65 REMARK 500 ASN A 154 0.30 83.28 REMARK 500 PRO A 319 46.89 -78.60 REMARK 500 ARG A 407 151.54 -47.05 REMARK 500 GLU A 415 1.46 -69.35 REMARK 500 PRO A 440 170.63 -58.62 REMARK 500 PHE B 45 -65.83 -129.14 REMARK 500 GLN B 89 1.14 82.31 REMARK 500 ASP B 191 -131.21 54.22 REMARK 500 PHE B 198 155.92 -43.67 REMARK 500 ALA B 204 1.58 82.29 REMARK 500 PRO B 228 -155.47 -79.48 REMARK 500 LYS B 229 14.64 53.41 REMARK 500 LYS B 315 -114.34 56.08 REMARK 500 SER B 415 -160.76 -121.66 REMARK 500 ASN B 435 -78.40 -110.83 REMARK 500 PHE B 436 25.79 -77.03 REMARK 500 GLU B 437 26.53 -73.94 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 MG B 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 507 O REMARK 620 2 ILE A 507 OXT 50.7 REMARK 620 N 1 DBREF1 8Z8Y A 1 507 UNP A0A1I7NFD7_9BACT DBREF2 8Z8Y A A0A1I7NFD7 1 507 DBREF1 8Z8Y B 1 450 UNP A0A1I7NFG5_9BACT DBREF2 8Z8Y B A0A1I7NFG5 1 450 SEQRES 1 A 507 MET LYS GLU LEU ILE TYR ILE GLU GLU PRO SER ILE LEU SEQRES 2 A 507 PHE ALA HIS GLY GLN LYS CYS THR ASP PRO ARG ASP GLY SEQRES 3 A 507 LEU ALA LEU PHE GLY PRO LEU ASN GLN ILE TYR GLY ILE SEQRES 4 A 507 LYS SER GLY VAL VAL GLY THR GLN LYS GLY LEU GLN ILE SEQRES 5 A 507 PHE LYS SER TYR LEU ASP LYS ILE GLN LYS PRO ILE TYR SEQRES 6 A 507 ASN HIS ASN ASN ILE THR ARG PRO MET PHE PRO GLY PHE SEQRES 7 A 507 GLU ALA VAL PHE GLY CYS LYS TRP GLU SER GLN ASN ILE SEQRES 8 A 507 VAL PHE LYS GLU ILE THR ASP GLU GLU ILE ARG ARG TYR SEQRES 9 A 507 LEU PHE ASN ALA SER THR HIS LYS ARG THR TYR ASP LEU SEQRES 10 A 507 VAL THR LEU PHE ASN ASP LYS ILE ILE THR ALA ASN LYS SEQRES 11 A 507 ASN ASP GLU GLU ARG VAL ASP VAL TRP PHE VAL ILE VAL SEQRES 12 A 507 PRO GLU GLU ILE TYR LYS TYR CYS ARG PRO ASN SER VAL SEQRES 13 A 507 LEU PRO ASN GLU LEU VAL GLN THR LYS SER LEU ILE SER SEQRES 14 A 507 LYS SER LYS ALA LYS SER PHE ARG TYR THR PRO THR LEU SEQRES 15 A 507 PHE GLU GLU PHE ASN LYS LYS LEU LYS GLU VAL GLU LYS SEQRES 16 A 507 GLU ALA LYS THR TYR ASN TYR ASP ALA GLN PHE HIS ASP SEQRES 17 A 507 GLN LEU LYS ALA ARG LEU LEU GLU HIS THR ILE PRO THR SEQRES 18 A 507 GLN ILE LEU ARG GLU SER THR LEU ALA TRP ARG ASP PHE SEQRES 19 A 507 LYS ASN THR PHE GLY ALA PRO ILE ARG ASP PHE SER LYS SEQRES 20 A 507 ILE GLU GLY HIS LEU ALA TRP THR ILE SER THR ALA ALA SEQRES 21 A 507 TYR TYR LYS ALA GLY GLY LYS PRO TRP LYS LEU GLY ASP SEQRES 22 A 507 ILE ARG PRO GLY VAL CYS TYR LEU GLY LEU VAL TYR LYS SEQRES 23 A 507 LYS ILE GLU LYS SER LYS ASN PRO GLN ASN ALA CYS CYS SEQRES 24 A 507 ALA ALA GLN MET PHE LEU ASP ASN GLY ASP GLY THR VAL SEQRES 25 A 507 PHE LYS GLY GLU VAL GLY PRO TRP TYR ASN PRO GLU LYS SEQRES 26 A 507 GLY GLU TYR HIS LEU LYS PRO LYS GLU ALA LYS ALA LEU SEQRES 27 A 507 LEU THR GLN ALA LEU GLU SER TYR LYS GLU GLN ASN LYS SEQRES 28 A 507 SER TYR PRO LYS GLU VAL PHE ILE HIS ALA ARG THR ARG SEQRES 29 A 507 PHE ASN ASP GLU GLU TRP ASN ALA PHE ASN GLU VAL THR SEQRES 30 A 507 PRO LYS ASN THR ASN LEU VAL GLY VAL THR ILE THR LYS SEQRES 31 A 507 SER LYS PRO LEU LYS LEU TYR LYS THR GLU GLY ALA PHE SEQRES 32 A 507 PRO ILE MET ARG GLY ASN ALA TYR ILE VAL ASP GLU LYS SEQRES 33 A 507 LYS ALA PHE LEU TRP THR LEU GLY PHE VAL PRO LYS LEU SEQRES 34 A 507 GLN SER THR LEU SER MET GLU VAL PRO ASN PRO ILE PHE SEQRES 35 A 507 ILE GLU ILE ASN LYS GLY GLU ALA GLU ILE GLN GLN VAL SEQRES 36 A 507 LEU LYS ASP ILE LEU ALA LEU THR LYS LEU ASN TYR ASN SEQRES 37 A 507 ALA CYS ILE TYR ALA ASP GLY GLU PRO VAL THR LEU ARG SEQRES 38 A 507 PHE ALA ASN LYS ILE GLY GLU ILE LEU THR ALA SER THR SEQRES 39 A 507 GLU ILE LYS THR PRO PRO LEU ALA PHE LYS TYR TYR ILE SEQRES 1 B 450 MET ARG ASN LYS ILE PHE ILE SER HIS ALA THR PRO GLU SEQRES 2 B 450 ASP ASP ASP PHE THR ARG TRP LEU SER LEU LYS LEU ILE SEQRES 3 B 450 GLY LEU GLY TYR GLU VAL TRP CYS ASP ILE LEU PHE LEU SEQRES 4 B 450 ASP LYS GLY VAL ASP PHE TRP SER THR ILE GLU LYS GLU SEQRES 5 B 450 ILE ARG GLU ASN THR CYS LYS PHE LEU ILE VAL SER SER SEQRES 6 B 450 THR ALA GLY ASN LYS ARG GLU GLY VAL LEU LYS GLU LEU SEQRES 7 B 450 ALA VAL ALA THR LYS VAL LYS LYS HIS LEU GLN ASP ASP SEQRES 8 B 450 MET PHE ILE ILE PRO LEU ALA ILE ASP GLU ASN LEU SER SEQRES 9 B 450 TYR ASP ASP ILE ASN ILE GLU ILE VAL ARG LEU ASN ALA SEQRES 10 B 450 ILE ASP PHE LYS LYS SER TRP ALA LYS GLY LEU GLN ASP SEQRES 11 B 450 LEU LEU ASP ALA PHE GLU LYS GLN ASN VAL PRO LYS LYS SEQRES 12 B 450 PRO PRO ASP HIS SER LYS SER ASN LEU LEU TYR GLN GLN SEQRES 13 B 450 ILE PHE LEU HIS ASP LYS GLN ALA ILE GLU LYS GLU GLU SEQRES 14 B 450 THR TYR ASP SER ASN TRP PHE PRO ILE ILE SER PHE PRO SEQRES 15 B 450 ASN GLU LEU ARG PHE HIS ARG TYR ASP TRP ARG LEU PRO SEQRES 16 B 450 LYS GLN PHE ASP VAL ARG THR LEU ALA PHE PRO ALA ILE SEQRES 17 B 450 ARG TYR LYS GLU TYR LEU CYS THR PHE ALA TRP GLU TYR SEQRES 18 B 450 ASP PHE ILE HIS GLN LEU PRO LYS THR GLU THR TYR ASN SEQRES 19 B 450 GLY GLN GLU SER ILE ARG ILE SER THR SER ASP ILE LEU SEQRES 20 B 450 SER GLY ARG TYR ASP THR ASP PHE ILE ARG ASN TYR GLU SEQRES 21 B 450 CYS GLN ARG LEU ILE VAL GLN LEU ILE ASN LYS ALA PHE SEQRES 22 B 450 GLU LEU ARG MET LYS ASP LYS ASN VAL ARG GLU TYR GLN SEQRES 23 B 450 MET SER LYS THR PHE ALA TYR TRP ILE GLU LYS GLY LYS SEQRES 24 B 450 LEU GLU LYS ASP LYS PHE GLU LYS ILE LYS LEU VAL GLY SEQRES 25 B 450 LYS GLN LYS ASN LYS TYR TRP HIS PHE GLY ILE SER ALA SEQRES 26 B 450 ALA GLY LYS LEU TYR PRO SER PRO VAL LEU MET VAL SER SEQRES 27 B 450 SER HIS ILE ILE PHE THR MET ASP GLY ILE ASN LEU ILE SEQRES 28 B 450 LYS SER LYS SER ILE GLN HIS SER SER ARG ARG LYS GLN SEQRES 29 B 450 GLY LYS ASN TRP TRP ASN ASP LYS TRP ARG GLU LYS LEU SEQRES 30 B 450 LEU ALA PHE ILE ARG PHE LEU SER ASP ASP GLN ASN ALA SEQRES 31 B 450 ILE TYR LEU ASN VAL GLY SER GLU GLU LYS ILE LEU ILE SEQRES 32 B 450 SER ASN LYS PRO LEU LYS PHE PHE GLY LYS MET SER TYR SEQRES 33 B 450 VAL THR PRO SER GLU VAL THR LEU GLU GLU GLU SER VAL SEQRES 34 B 450 LEU ALA ASP ILE ASN ASN PHE GLU GLU ASP THR GLU ASP SEQRES 35 B 450 LEU ASP GLU LEU GLU ASP ILE GLU HET MG A 601 1 HET MG B 501 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *7(H2 O) HELIX 1 AA1 ALA A 15 GLY A 17 5 3 HELIX 2 AA2 ASP A 22 GLY A 31 1 10 HELIX 3 AA3 THR A 46 LYS A 62 1 17 HELIX 4 AA4 GLY A 77 GLY A 83 1 7 HELIX 5 AA5 THR A 97 PHE A 106 1 10 HELIX 6 AA6 SER A 109 ASP A 132 1 24 HELIX 7 AA7 PRO A 144 CYS A 151 1 8 HELIX 8 AA8 PRO A 158 VAL A 162 5 5 HELIX 9 AA9 SER A 169 LYS A 174 1 6 HELIX 10 AB1 PHE A 183 THR A 199 1 17 HELIX 11 AB2 GLN A 205 LEU A 215 1 11 HELIX 12 AB3 GLU A 216 THR A 218 5 3 HELIX 13 AB4 GLU A 226 ALA A 230 1 5 HELIX 14 AB5 ILE A 248 GLY A 265 1 18 HELIX 15 AB6 LYS A 331 LYS A 351 1 21 HELIX 16 AB7 ASN A 366 GLU A 375 1 10 HELIX 17 AB8 GLU A 451 LEU A 465 1 15 HELIX 18 AB9 PRO A 477 PHE A 482 1 6 HELIX 19 AC1 PHE A 482 SER A 493 1 12 HELIX 20 AC2 LYS A 504 ILE A 507 5 4 HELIX 21 AC3 ASP B 14 GLY B 29 1 16 HELIX 22 AC4 CYS B 34 PHE B 38 5 5 HELIX 23 AC5 PHE B 45 ASN B 56 1 12 HELIX 24 AC6 SER B 65 ARG B 71 1 7 HELIX 25 AC7 ARG B 71 GLN B 89 1 19 HELIX 26 AC8 ASP B 90 MET B 92 5 3 HELIX 27 AC9 ASN B 109 LEU B 115 1 7 HELIX 28 AD1 SER B 123 ASN B 139 1 17 HELIX 29 AD2 HIS B 147 PHE B 158 1 12 HELIX 30 AD3 TYR B 190 LEU B 194 5 5 HELIX 31 AD4 ASP B 199 LEU B 203 5 5 HELIX 32 AD5 TRP B 219 PHE B 223 5 5 HELIX 33 AD6 ASN B 234 SER B 238 5 5 HELIX 34 AD7 THR B 243 SER B 248 1 6 HELIX 35 AD8 ARG B 257 LYS B 280 1 24 HELIX 36 AD9 LEU B 300 LYS B 302 5 3 HELIX 37 AE1 SER B 353 ASN B 367 1 15 HELIX 38 AE2 TRP B 369 LEU B 378 1 10 HELIX 39 AE3 LEU B 378 LEU B 384 1 7 HELIX 40 AE4 GLU B 421 VAL B 429 1 9 SHEET 1 AA112 LEU A 501 ALA A 502 0 SHEET 2 AA112 THR A 311 LYS A 314 -1 N VAL A 312 O LEU A 501 SHEET 3 AA112 ALA A 297 PHE A 304 -1 N ALA A 301 O PHE A 313 SHEET 4 AA112 VAL A 278 LYS A 287 -1 N TYR A 280 O PHE A 304 SHEET 5 AA112 GLU A 356 ALA A 361 1 O PHE A 358 N CYS A 279 SHEET 6 AA112 ASN A 382 THR A 389 1 O VAL A 386 N ILE A 359 SHEET 7 AA112 ILE A 441 LYS A 447 -1 O LYS A 447 N GLY A 385 SHEET 8 AA112 LYS A 417 LEU A 420 -1 N ALA A 418 O ILE A 443 SHEET 9 AA112 ASN A 409 ASP A 414 -1 N TYR A 411 O PHE A 419 SHEET 10 AA112 GLU A 3 TYR A 6 -1 N ILE A 5 O ALA A 410 SHEET 11 AA112 PHE B 410 GLY B 412 1 O PHE B 411 N LEU A 4 SHEET 12 AA112 GLU B 169 TYR B 171 -1 N GLU B 169 O GLY B 412 SHEET 1 AA2 3 LYS A 19 CYS A 20 0 SHEET 2 AA2 3 ILE A 12 LEU A 13 -1 N ILE A 12 O CYS A 20 SHEET 3 AA2 3 LYS A 270 LEU A 271 -1 O LYS A 270 N LEU A 13 SHEET 1 AA3 4 ILE A 91 GLU A 95 0 SHEET 2 AA3 4 SER A 41 GLY A 45 1 N VAL A 43 O VAL A 92 SHEET 3 AA3 4 VAL A 138 VAL A 143 1 O PHE A 140 N GLY A 42 SHEET 4 AA3 4 THR A 221 ARG A 225 1 O GLN A 222 N VAL A 141 SHEET 1 AA4 2 TYR A 321 ASN A 322 0 SHEET 2 AA4 2 GLU A 327 TYR A 328 -1 O GLU A 327 N ASN A 322 SHEET 1 AA5 2 PHE A 425 VAL A 426 0 SHEET 2 AA5 2 SER A 431 THR A 432 -1 O SER A 431 N VAL A 426 SHEET 1 AA6 3 LYS B 4 ILE B 7 0 SHEET 2 AA6 3 THR B 57 LEU B 61 1 O CYS B 58 N LYS B 4 SHEET 3 AA6 3 ILE B 94 ILE B 95 1 O ILE B 95 N PHE B 60 SHEET 1 AA7 2 LEU B 97 ALA B 98 0 SHEET 2 AA7 2 ILE B 118 ASP B 119 1 O ILE B 118 N ALA B 98 SHEET 1 AA8 5 ALA B 326 LYS B 328 0 SHEET 2 AA8 5 VAL B 334 MET B 336 -1 O VAL B 334 N LYS B 328 SHEET 3 AA8 5 TRP B 175 SER B 180 -1 N PHE B 176 O LEU B 335 SHEET 4 AA8 5 LYS B 400 SER B 404 -1 O LEU B 402 N SER B 180 SHEET 5 AA8 5 ALA B 390 ASN B 394 -1 N LEU B 393 O ILE B 401 SHEET 1 AA9 4 ALA B 207 ARG B 209 0 SHEET 2 AA9 4 LEU B 214 THR B 216 -1 O CYS B 215 N ILE B 208 SHEET 3 AA9 4 GLU B 184 HIS B 188 -1 N ARG B 186 O THR B 216 SHEET 4 AA9 4 ILE B 239 SER B 242 -1 O ILE B 241 N LEU B 185 SHEET 1 AB1 2 ARG B 283 GLN B 286 0 SHEET 2 AB1 2 PHE B 291 TRP B 294 -1 O ALA B 292 N TYR B 285 SHEET 1 AB2 2 LYS B 304 PHE B 305 0 SHEET 2 AB2 2 ILE B 308 LYS B 309 -1 O ILE B 308 N PHE B 305 SHEET 1 AB3 3 VAL B 311 GLN B 314 0 SHEET 2 AB3 3 LYS B 317 ILE B 323 -1 O LYS B 317 N GLN B 314 SHEET 3 AB3 3 SER B 339 THR B 344 -1 O THR B 344 N TYR B 318 LINK O ILE A 507 MG MG B 501 1555 1555 2.64 LINK OXT ILE A 507 MG MG B 501 1555 1555 1.91 CISPEP 1 THR B 11 PRO B 12 0 4.60 CISPEP 2 TYR B 330 PRO B 331 0 4.76 CRYST1 198.360 198.360 184.350 90.00 90.00 120.00 P 65 2 2 12 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 0.005041 0.002911 0.000000 0.00000 SCALE2 0.000000 0.005821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005424 0.00000