HEADER HYDROLASE 01-JUN-16 5L6Z TITLE CRYSTAL STRUCTURE OF D62A MUTANT OF THERMOTOGA MARITIMA TMPEP1050 TITLE 2 AMINOPEPTIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCYLAMINOPEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ENDOGLUCANASE M; COMPND 5 EC: 3.2.1.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA (STRAIN ATCC 43589 / MSB8 / SOURCE 3 DSM 3109 / JCM 10099); SOURCE 4 ORGANISM_TAXID: 243274; SOURCE 5 STRAIN: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099; SOURCE 6 ATCC: 43589; SOURCE 7 GENE: TM_1050, TMARI_1054; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: MC1061; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PCEC85 KEYWDS LEUCYLAMINOPEPTIDASE, M42 FAMILY, TETRAHEDRAL STRUCTURE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.DUTOIT,D.VAN ELDER,C.BAUVOIS REVDAT 3 10-JAN-24 5L6Z 1 REMARK REVDAT 2 24-FEB-21 5L6Z 1 JRNL ATOM REVDAT 1 21-JUN-17 5L6Z 0 JRNL AUTH R.DUTOIT,N.BRANDT,T.VAN GOMPEL,D.VAN ELDER,J.VAN DYCK, JRNL AUTH 2 F.SOBOTT,L.DROOGMANS JRNL TITL M42 AMINOPEPTIDASE CATALYTIC SITE: THE STRUCTURAL AND JRNL TITL 2 FUNCTIONAL ROLE OF A STRICTLY CONSERVED ASPARTATE RESIDUE JRNL REF PROTEINS 2020 JRNL REFN ESSN 1097-0134 JRNL DOI 10.1002/PROT.25982 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.DUTOIT,N.BRANDT,C.LEGRAIN,C.BAUVOIS REMARK 1 TITL FUNCTIONAL CHARACTERIZATION OF TWO M42 AMINOPEPTIDASES REMARK 1 TITL 2 ERRONEOUSLY ANNOTATED AS CELLULASES. REMARK 1 REF PLOS ONE V. 7 50639 2012 REMARK 1 REFN ESSN 1932-6203 REMARK 1 PMID 23226342 REMARK 1 DOI 10.1371/JOURNAL.PONE.0050639 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.10.1-2155-000 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 103177 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5159 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 48.0243 - 4.6626 0.98 3460 183 0.1747 0.1871 REMARK 3 2 4.6626 - 3.7013 1.00 3404 179 0.1363 0.1599 REMARK 3 3 3.7013 - 3.2335 1.00 3310 174 0.1507 0.1933 REMARK 3 4 3.2335 - 2.9379 1.00 3326 175 0.1640 0.1854 REMARK 3 5 2.9379 - 2.7274 1.00 3312 175 0.1752 0.2142 REMARK 3 6 2.7274 - 2.5666 1.00 3299 173 0.1811 0.2256 REMARK 3 7 2.5666 - 2.4380 1.00 3260 172 0.1811 0.2201 REMARK 3 8 2.4380 - 2.3319 1.00 3285 173 0.1864 0.1982 REMARK 3 9 2.3319 - 2.2421 1.00 3282 172 0.1821 0.2097 REMARK 3 10 2.2421 - 2.1648 1.00 3294 174 0.1830 0.2103 REMARK 3 11 2.1648 - 2.0971 1.00 3242 170 0.1931 0.1933 REMARK 3 12 2.0971 - 2.0371 1.00 3276 173 0.2003 0.2672 REMARK 3 13 2.0371 - 1.9835 1.00 3273 172 0.2015 0.2191 REMARK 3 14 1.9835 - 1.9351 1.00 3231 170 0.1958 0.2459 REMARK 3 15 1.9351 - 1.8911 1.00 3249 171 0.2026 0.2339 REMARK 3 16 1.8911 - 1.8509 1.00 3271 171 0.2034 0.2408 REMARK 3 17 1.8509 - 1.8139 1.00 3253 172 0.2087 0.2603 REMARK 3 18 1.8139 - 1.7796 1.00 3248 170 0.2054 0.2440 REMARK 3 19 1.7796 - 1.7478 1.00 3261 172 0.2089 0.2695 REMARK 3 20 1.7478 - 1.7182 1.00 3270 172 0.2194 0.2259 REMARK 3 21 1.7182 - 1.6905 1.00 3176 168 0.2161 0.2718 REMARK 3 22 1.6905 - 1.6645 1.00 3317 174 0.2098 0.2592 REMARK 3 23 1.6645 - 1.6400 1.00 3182 168 0.2116 0.2325 REMARK 3 24 1.6400 - 1.6169 1.00 3280 172 0.2088 0.2684 REMARK 3 25 1.6169 - 1.5951 1.00 3237 171 0.2159 0.2760 REMARK 3 26 1.5951 - 1.5743 1.00 3240 170 0.2157 0.2550 REMARK 3 27 1.5743 - 1.5547 1.00 3194 168 0.2204 0.2525 REMARK 3 28 1.5547 - 1.5359 1.00 3291 173 0.2227 0.2775 REMARK 3 29 1.5359 - 1.5181 1.00 3174 168 0.2283 0.2428 REMARK 3 30 1.5181 - 1.5010 0.95 3121 164 0.2356 0.2524 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.20 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 : 0.006 5099 REMARK 3 ANGLE : 0.821 6946 REMARK 3 CHIRALITY : 0.057 791 REMARK 3 PLANARITY : 0.006 929 REMARK 3 DIHEDRAL : 14.040 3107 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 5L6Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000214. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 103936 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 48.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.510 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.0 REMARK 200 STARTING MODEL: 4P6Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 5% PEG3350 (V/V) REMARK 280 PH5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 133.61500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 133.61500 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 21.09000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.98000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 21.09000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.98000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 133.61500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 21.09000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.98000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 133.61500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 21.09000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.98000 REMARK 290 SMTRY3 8 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: 1940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 436 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 553 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 703 LIES ON A SPECIAL POSITION. 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 LEU A 201 REMARK 465 VAL A 202 REMARK 465 GLY A 203 REMARK 465 ALA A 204 REMARK 465 SER A 205 REMARK 465 VAL A 206 REMARK 465 ALA A 207 REMARK 465 GLY A 208 REMARK 465 GLY A 280 REMARK 465 GLY A 281 REMARK 465 THR A 282 REMARK 465 ASN A 283 REMARK 465 ALA A 284 REMARK 465 MET A 285 REMARK 465 GLY A 286 REMARK 465 TYR A 287 REMARK 465 GLN A 288 REMARK 465 ARG A 289 REMARK 465 THR A 290 REMARK 465 ARG A 291 REMARK 465 GLU A 292 REMARK 465 SER B 205 REMARK 465 VAL B 206 REMARK 465 ALA B 207 REMARK 465 THR B 278 REMARK 465 PHE B 279 REMARK 465 GLY B 280 REMARK 465 GLY B 281 REMARK 465 THR B 282 REMARK 465 ASN B 283 REMARK 465 ALA B 284 REMARK 465 MET B 285 REMARK 465 GLY B 286 REMARK 465 TYR B 287 REMARK 465 GLN B 288 REMARK 465 ARG B 289 REMARK 465 THR B 290 REMARK 465 ARG B 291 REMARK 465 GLU B 292 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 GLU A 52 CD OE1 OE2 REMARK 470 LYS A 54 CD CE NZ REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 ARG A 120 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 LYS A 141 CG CD CE NZ REMARK 470 LYS A 184 CE NZ REMARK 470 ILE A 231 CG1 CG2 CD1 REMARK 470 LYS A 232 CG CD CE NZ REMARK 470 ARG A 233 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 247 CD CE NZ REMARK 470 ARG A 249 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 255 CD CE NZ REMARK 470 LYS A 271 CD CE NZ REMARK 470 GLU B 117 CD OE1 OE2 REMARK 470 ARG B 120 NE CZ NH1 NH2 REMARK 470 LYS B 121 CG CD CE NZ REMARK 470 LYS B 141 CG CD CE NZ REMARK 470 GLU B 197 CG CD OE1 OE2 REMARK 470 ILE B 231 CG1 CG2 CD1 REMARK 470 LYS B 232 CG CD CE NZ REMARK 470 ARG B 233 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 247 CE NZ REMARK 470 ASP B 248 CG OD1 OD2 REMARK 470 ARG B 249 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 271 CE NZ REMARK 470 LEU B 277 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 O HOH B 614 O HOH B 713 1.80 REMARK 500 O HOH B 625 O HOH B 742 1.82 REMARK 500 O HOH A 601 O HOH A 821 1.82 REMARK 500 O HOH A 542 O HOH A 828 1.83 REMARK 500 O HOH A 848 O HOH A 856 1.84 REMARK 500 O GLY B 293 O HOH B 401 1.84 REMARK 500 O HOH A 648 O HOH A 864 1.86 REMARK 500 O HOH B 760 O HOH B 797 1.88 REMARK 500 O HOH A 742 O HOH A 783 1.88 REMARK 500 O HOH A 822 O HOH A 888 1.89 REMARK 500 O HOH A 872 O HOH A 890 1.90 REMARK 500 O HOH B 411 O HOH B 588 1.92 REMARK 500 O HOH B 696 O HOH B 797 1.92 REMARK 500 O HOH A 682 O HOH A 808 1.92 REMARK 500 O HOH B 411 O HOH B 495 1.97 REMARK 500 O HOH A 791 O HOH A 871 1.98 REMARK 500 O HOH B 647 O HOH B 668 1.99 REMARK 500 O HOH A 589 O HOH A 844 1.99 REMARK 500 O HOH A 773 O HOH A 811 2.00 REMARK 500 O HOH A 777 O HOH A 865 2.00 REMARK 500 O HOH A 564 O HOH A 656 2.01 REMARK 500 O HOH A 525 O HOH A 770 2.01 REMARK 500 O HOH B 706 O HOH B 733 2.01 REMARK 500 O HOH A 567 O HOH A 769 2.02 REMARK 500 O HOH A 787 O HOH A 861 2.03 REMARK 500 O HOH B 417 O HOH B 653 2.03 REMARK 500 O HOH B 481 O HOH B 745 2.03 REMARK 500 O HOH A 675 O HOH A 884 2.03 REMARK 500 O HOH B 453 O HOH B 725 2.04 REMARK 500 O HOH A 553 O HOH A 557 2.04 REMARK 500 O HOH B 427 O HOH B 608 2.04 REMARK 500 OE1 GLU A 30 O HOH A 501 2.04 REMARK 500 O HOH A 527 O HOH A 589 2.04 REMARK 500 O HOH B 421 O HOH B 772 2.05 REMARK 500 O HOH A 802 O HOH A 841 2.06 REMARK 500 O HOH A 829 O HOH A 898 2.06 REMARK 500 O HOH A 568 O HOH A 731 2.06 REMARK 500 O HOH B 694 O HOH B 714 2.06 REMARK 500 NZ LYS B 2 O HOH B 402 2.07 REMARK 500 O HOH A 777 O HOH A 812 2.07 REMARK 500 NZ LYS A 74 O HOH A 502 2.08 REMARK 500 O HOH A 837 O HOH A 847 2.08 REMARK 500 O HOH A 668 O HOH A 733 2.08 REMARK 500 O HOH A 510 O HOH A 749 2.08 REMARK 500 O1 CIT A 401 O HOH A 503 2.08 REMARK 500 O HOH A 752 O HOH A 863 2.09 REMARK 500 OD1 ASP A 73 NH2 ARG A 136 2.09 REMARK 500 O HOH A 839 O HOH A 890 2.09 REMARK 500 N ILE A 231 O HOH A 504 2.11 REMARK 500 O HOH A 880 O HOH A 903 2.12 REMARK 500 REMARK 500 THIS ENTRY HAS 79 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 HOH A 515 O HOH B 437 5445 1.58 REMARK 500 O HOH A 849 O HOH B 566 5445 1.82 REMARK 500 O HOH A 855 O HOH B 596 1655 1.83 REMARK 500 O HOH A 888 O HOH B 751 5545 1.84 REMARK 500 O HOH A 842 O HOH B 676 5545 1.90 REMARK 500 O HOH A 619 O HOH B 530 1655 1.91 REMARK 500 O HOH A 558 O HOH B 557 5545 1.91 REMARK 500 O HOH A 815 O HOH B 782 5545 2.11 REMARK 500 O GLY A 92 O HOH B 404 5545 2.18 REMARK 500 O HOH A 849 O HOH B 523 5445 2.18 REMARK 500 O HOH A 901 O HOH B 670 5545 2.18 REMARK 500 O HOH A 845 O HOH B 607 5545 2.18 REMARK 500 O HOH A 774 O HOH B 732 5445 2.18 REMARK 500 O HOH B 409 O HOH B 425 31057 2.19 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 CYS A 143 73.95 -152.97 REMARK 500 CYS B 143 75.19 -153.25 REMARK 500 SER B 159 59.89 39.15 REMARK 500 TYR B 209 -147.98 61.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 906 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A 907 DISTANCE = 7.14 ANGSTROMS REMARK 525 HOH B 812 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH B 813 DISTANCE = 6.59 ANGSTROMS 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 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 26 O REMARK 620 2 GLU A 30 OE1 100.5 REMARK 620 3 HOH A 818 O 152.8 76.4 REMARK 620 4 HOH A 826 O 106.9 74.8 98.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 168 O REMARK 620 2 HOH A 571 O 87.7 REMARK 620 3 HOH A 778 O 131.1 98.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P6Y RELATED DB: PDB REMARK 900 4P6Y IS THE STRUCTURE OF TMPEP1050. THE WILD-TYPE ENZYME ADOPTS A REMARK 900 TETRAHEDRAL-SHAPED STRUCTURE WITH 12 SUB-UNITS. DBREF 5L6Z A 1 331 UNP Q9X0E0 Q9X0E0_THEMA 1 331 DBREF 5L6Z B 1 331 UNP Q9X0E0 Q9X0E0_THEMA 1 331 SEQADV 5L6Z ALA A 62 UNP Q9X0E0 ASP 62 ENGINEERED MUTATION SEQADV 5L6Z ALA B 62 UNP Q9X0E0 ASP 62 ENGINEERED MUTATION SEQRES 1 A 331 MET LYS GLU LEU ILE ARG LYS LEU THR GLU ALA PHE GLY SEQRES 2 A 331 PRO SER GLY ARG GLU GLU GLU VAL ARG SER ILE ILE LEU SEQRES 3 A 331 GLU GLU LEU GLU GLY HIS ILE ASP GLY HIS ARG ILE ASP SEQRES 4 A 331 GLY LEU GLY ASN LEU ILE VAL TRP LYS GLY SER GLY GLU SEQRES 5 A 331 LYS LYS VAL ILE LEU ASP ALA HIS ILE ALA GLU ILE GLY SEQRES 6 A 331 VAL VAL VAL THR ASN VAL ASP ASP LYS GLY PHE LEU THR SEQRES 7 A 331 ILE GLU PRO VAL GLY GLY VAL SER PRO TYR MET LEU LEU SEQRES 8 A 331 GLY LYS ARG ILE ARG PHE GLU ASN GLY THR ILE GLY VAL SEQRES 9 A 331 VAL GLY MET GLU GLY GLU THR THR GLU GLU ARG GLN GLU SEQRES 10 A 331 ASN VAL ARG LYS LEU SER PHE ASP LYS LEU PHE ILE ASP SEQRES 11 A 331 ILE GLY ALA ASN SER ARG GLU GLU ALA GLN LYS MET CYS SEQRES 12 A 331 PRO ILE GLY SER PHE GLY VAL TYR ASP SER GLY PHE VAL SEQRES 13 A 331 GLU VAL SER GLY LYS TYR VAL SER LYS ALA MET ASP ASP SEQRES 14 A 331 ARG ILE GLY CYS ALA VAL ILE VAL GLU VAL PHE LYS ARG SEQRES 15 A 331 ILE LYS PRO ALA VAL THR LEU TYR GLY VAL PHE SER VAL SEQRES 16 A 331 GLN GLU GLU VAL GLY LEU VAL GLY ALA SER VAL ALA GLY SEQRES 17 A 331 TYR GLY VAL PRO ALA ASP GLU ALA ILE ALA ILE ASP VAL SEQRES 18 A 331 THR ASP SER ALA ASP THR PRO LYS ALA ILE LYS ARG HIS SEQRES 19 A 331 ALA MET ARG LEU SER GLY GLY PRO ALA LEU LYS VAL LYS SEQRES 20 A 331 ASP ARG ALA SER ILE SER SER LYS ARG ILE LEU GLU ASN SEQRES 21 A 331 LEU ILE GLU ILE ALA GLU LYS PHE ASP ILE LYS TYR GLN SEQRES 22 A 331 MET GLU VAL LEU THR PHE GLY GLY THR ASN ALA MET GLY SEQRES 23 A 331 TYR GLN ARG THR ARG GLU GLY ILE PRO SER ALA THR VAL SEQRES 24 A 331 SER ILE PRO THR ARG TYR VAL HIS SER PRO SER GLU MET SEQRES 25 A 331 ILE ALA PRO ASP ASP VAL GLU ALA THR VAL ASP LEU LEU SEQRES 26 A 331 ILE ARG TYR LEU GLY ALA SEQRES 1 B 331 MET LYS GLU LEU ILE ARG LYS LEU THR GLU ALA PHE GLY SEQRES 2 B 331 PRO SER GLY ARG GLU GLU GLU VAL ARG SER ILE ILE LEU SEQRES 3 B 331 GLU GLU LEU GLU GLY HIS ILE ASP GLY HIS ARG ILE ASP SEQRES 4 B 331 GLY LEU GLY ASN LEU ILE VAL TRP LYS GLY SER GLY GLU SEQRES 5 B 331 LYS LYS VAL ILE LEU ASP ALA HIS ILE ALA GLU ILE GLY SEQRES 6 B 331 VAL VAL VAL THR ASN VAL ASP ASP LYS GLY PHE LEU THR SEQRES 7 B 331 ILE GLU PRO VAL GLY GLY VAL SER PRO TYR MET LEU LEU SEQRES 8 B 331 GLY LYS ARG ILE ARG PHE GLU ASN GLY THR ILE GLY VAL SEQRES 9 B 331 VAL GLY MET GLU GLY GLU THR THR GLU GLU ARG GLN GLU SEQRES 10 B 331 ASN VAL ARG LYS LEU SER PHE ASP LYS LEU PHE ILE ASP SEQRES 11 B 331 ILE GLY ALA ASN SER ARG GLU GLU ALA GLN LYS MET CYS SEQRES 12 B 331 PRO ILE GLY SER PHE GLY VAL TYR ASP SER GLY PHE VAL SEQRES 13 B 331 GLU VAL SER GLY LYS TYR VAL SER LYS ALA MET ASP ASP SEQRES 14 B 331 ARG ILE GLY CYS ALA VAL ILE VAL GLU VAL PHE LYS ARG SEQRES 15 B 331 ILE LYS PRO ALA VAL THR LEU TYR GLY VAL PHE SER VAL SEQRES 16 B 331 GLN GLU GLU VAL GLY LEU VAL GLY ALA SER VAL ALA GLY SEQRES 17 B 331 TYR GLY VAL PRO ALA ASP GLU ALA ILE ALA ILE ASP VAL SEQRES 18 B 331 THR ASP SER ALA ASP THR PRO LYS ALA ILE LYS ARG HIS SEQRES 19 B 331 ALA MET ARG LEU SER GLY GLY PRO ALA LEU LYS VAL LYS SEQRES 20 B 331 ASP ARG ALA SER ILE SER SER LYS ARG ILE LEU GLU ASN SEQRES 21 B 331 LEU ILE GLU ILE ALA GLU LYS PHE ASP ILE LYS TYR GLN SEQRES 22 B 331 MET GLU VAL LEU THR PHE GLY GLY THR ASN ALA MET GLY SEQRES 23 B 331 TYR GLN ARG THR ARG GLU GLY ILE PRO SER ALA THR VAL SEQRES 24 B 331 SER ILE PRO THR ARG TYR VAL HIS SER PRO SER GLU MET SEQRES 25 B 331 ILE ALA PRO ASP ASP VAL GLU ALA THR VAL ASP LEU LEU SEQRES 26 B 331 ILE ARG TYR LEU GLY ALA HET CIT A 401 26 HET NA A 402 1 HET NA A 403 1 HETNAM CIT CITRIC ACID HETNAM NA SODIUM ION FORMUL 3 CIT C6 H8 O7 FORMUL 4 NA 2(NA 1+) FORMUL 6 HOH *820(H2 O) HELIX 1 AA1 MET A 1 ALA A 11 1 11 HELIX 2 AA2 GLU A 18 GLU A 30 1 13 HELIX 3 AA3 SER A 86 LEU A 90 5 5 HELIX 4 AA4 THR A 111 LYS A 121 1 11 HELIX 5 AA5 SER A 123 ASP A 125 5 3 HELIX 6 AA6 SER A 135 CYS A 143 1 9 HELIX 7 AA7 ALA A 166 ILE A 183 1 18 HELIX 8 AA8 VAL A 195 GLY A 200 5 6 HELIX 9 AA9 SER A 251 PHE A 268 1 18 HELIX 10 AB1 ALA A 314 GLY A 330 1 17 HELIX 11 AB2 LYS B 2 ALA B 11 1 10 HELIX 12 AB3 GLU B 18 GLU B 30 1 13 HELIX 13 AB4 SER B 86 LEU B 90 5 5 HELIX 14 AB5 THR B 111 LYS B 121 1 11 HELIX 15 AB6 SER B 123 ASP B 125 5 3 HELIX 16 AB7 SER B 135 CYS B 143 1 9 HELIX 17 AB8 ALA B 166 ILE B 183 1 18 HELIX 18 AB9 SER B 251 PHE B 268 1 18 HELIX 19 AC1 ALA B 314 GLY B 330 1 17 SHEET 1 AA1 8 GLY A 35 ILE A 38 0 SHEET 2 AA1 8 LEU A 44 LYS A 48 -1 O ILE A 45 N ARG A 37 SHEET 3 AA1 8 THR A 188 SER A 194 -1 O PHE A 193 N LEU A 44 SHEET 4 AA1 8 LYS A 54 HIS A 60 1 N VAL A 55 O TYR A 190 SHEET 5 AA1 8 GLU A 215 ASP A 223 1 O ILE A 219 N ASP A 58 SHEET 6 AA1 8 SER A 296 THR A 303 1 O VAL A 299 N ALA A 218 SHEET 7 AA1 8 ALA A 243 LYS A 245 -1 N ALA A 243 O SER A 300 SHEET 8 AA1 8 GLN A 273 GLU A 275 1 O GLN A 273 N LEU A 244 SHEET 1 AA2 7 GLY A 65 VAL A 71 0 SHEET 2 AA2 7 LEU A 77 VAL A 82 -1 O THR A 78 N THR A 69 SHEET 3 AA2 7 LEU A 127 ASP A 130 -1 O ILE A 129 N LEU A 77 SHEET 4 AA2 7 ILE A 102 MET A 107 -1 N VAL A 104 O ASP A 130 SHEET 5 AA2 7 ARG A 94 PHE A 97 -1 N ILE A 95 O GLY A 103 SHEET 6 AA2 7 PHE A 148 TYR A 151 -1 O VAL A 150 N ARG A 96 SHEET 7 AA2 7 GLY A 65 VAL A 71 -1 N VAL A 66 O GLY A 149 SHEET 1 AA3 3 VAL A 156 VAL A 158 0 SHEET 2 AA3 3 LYS A 161 SER A 164 -1 O VAL A 163 N VAL A 156 SHEET 3 AA3 3 GLU A 311 ILE A 313 -1 O ILE A 313 N TYR A 162 SHEET 1 AA4 8 GLY B 35 ILE B 38 0 SHEET 2 AA4 8 LEU B 44 LYS B 48 -1 O ILE B 45 N ARG B 37 SHEET 3 AA4 8 THR B 188 SER B 194 -1 O LEU B 189 N LYS B 48 SHEET 4 AA4 8 LYS B 54 HIS B 60 1 N VAL B 55 O TYR B 190 SHEET 5 AA4 8 GLU B 215 ASP B 223 1 O ILE B 217 N ILE B 56 SHEET 6 AA4 8 SER B 296 THR B 303 1 O VAL B 299 N ALA B 218 SHEET 7 AA4 8 ALA B 243 VAL B 246 -1 N ALA B 243 O SER B 300 SHEET 8 AA4 8 GLN B 273 VAL B 276 1 O GLU B 275 N VAL B 246 SHEET 1 AA5 7 GLY B 65 VAL B 71 0 SHEET 2 AA5 7 LEU B 77 VAL B 82 -1 O VAL B 82 N GLY B 65 SHEET 3 AA5 7 LEU B 127 ASP B 130 -1 O ILE B 129 N LEU B 77 SHEET 4 AA5 7 ILE B 102 MET B 107 -1 N VAL B 104 O ASP B 130 SHEET 5 AA5 7 ARG B 94 PHE B 97 -1 N ILE B 95 O GLY B 103 SHEET 6 AA5 7 PHE B 148 TYR B 151 -1 O VAL B 150 N ARG B 96 SHEET 7 AA5 7 GLY B 65 VAL B 71 -1 N VAL B 66 O GLY B 149 SHEET 1 AA6 3 VAL B 156 VAL B 158 0 SHEET 2 AA6 3 LYS B 161 SER B 164 -1 O VAL B 163 N VAL B 156 SHEET 3 AA6 3 GLU B 311 ILE B 313 -1 O ILE B 313 N TYR B 162 LINK O LEU A 26 NA NA A 402 1555 1555 2.73 LINK OE1BGLU A 30 NA NA A 402 1555 1555 2.92 LINK O ASP A 168 NA NA A 403 1555 1555 2.78 LINK NA NA A 402 O HOH A 818 1555 1555 2.75 LINK NA NA A 402 O HOH A 826 1555 1555 2.96 LINK NA NA A 403 O HOH A 571 1555 1555 2.84 LINK NA NA A 403 O HOH A 778 1555 1555 2.73 CISPEP 1 ASP A 168 ASP A 169 0 0.48 CISPEP 2 ASP B 168 ASP B 169 0 0.76 SITE 1 AC1 15 LYS A 93 ARG A 94 ASP A 152 SER A 153 SITE 2 AC1 15 HOH A 503 HOH A 505 HOH A 509 HOH A 517 SITE 3 AC1 15 HOH A 582 LYS B 93 ARG B 94 ASP B 152 SITE 4 AC1 15 SER B 153 PRO B 309 HOH B 404 SITE 1 AC2 4 LEU A 26 GLU A 30 HOH A 818 HOH A 826 SITE 1 AC3 5 GLU A 63 ILE A 64 ASP A 168 HOH A 571 SITE 2 AC3 5 HOH A 778 CRYST1 42.180 113.960 267.230 90.00 90.00 90.00 C 2 2 21 16 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 0.023708 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003742 0.00000