HEADER BIOSYNTHETIC PROTEIN 11-FEB-20 6VSD TITLE MYCOBACTERIUM TUBERCULOSIS DIHYDROFOLATE REDUCTASE IN COMPLEX WITH 3- TITLE 2 ((THIOPHEN-2-YLTHIO)METHYL)BENZOIC ACID (FRAGMENT 13) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.5.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: FOLA, DFRA, RV2763C, MTV002.28C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS FOLATE PATHWAY, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.A.RIBEIRO,M.V.B.DIAS REVDAT 3 11-OCT-23 6VSD 1 REMARK REVDAT 2 26-AUG-20 6VSD 1 JRNL LINK REVDAT 1 15-JUL-20 6VSD 0 JRNL AUTH J.A.RIBEIRO,A.HAMMER,G.A.LIBREROS-ZUNIGA,S.M.CHAVEZ-PACHECO, JRNL AUTH 2 P.TYRAKIS,G.S.DE OLIVEIRA,T.KIRKMAN,J.EL BAKALI,S.A.ROCCO, JRNL AUTH 3 M.L.SFORCA,R.PARISE-FILHO,A.G.COYNE,T.L.BLUNDELL,C.ABELL, JRNL AUTH 4 M.V.B.DIAS JRNL TITL USING A FRAGMENT-BASED APPROACH TO IDENTIFY ALTERNATIVE JRNL TITL 2 CHEMICAL SCAFFOLDS TARGETING DIHYDROFOLATE REDUCTASE JRNL TITL 3 FROMMYCOBACTERIUM TUBERCULOSIS. JRNL REF ACS INFECT DIS. V. 6 2192 2020 JRNL REFN ESSN 2373-8227 JRNL PMID 32603583 JRNL DOI 10.1021/ACSINFECDIS.0C00263 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 35710 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1844 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 17.8563 - 3.9736 0.94 2754 162 0.1153 0.1484 REMARK 3 2 3.9736 - 3.1597 0.95 2662 148 0.1228 0.1860 REMARK 3 3 3.1597 - 2.7619 0.94 2600 168 0.1558 0.1975 REMARK 3 4 2.7619 - 2.5102 0.96 2654 115 0.1783 0.2343 REMARK 3 5 2.5102 - 2.3307 0.96 2626 112 0.1923 0.2425 REMARK 3 6 2.3307 - 2.1935 0.96 2593 117 0.2057 0.2468 REMARK 3 7 2.1935 - 2.0838 0.95 2597 146 0.2152 0.2271 REMARK 3 8 2.0838 - 1.9932 0.94 2557 151 0.2359 0.2750 REMARK 3 9 1.9932 - 1.9166 0.95 2590 145 0.2406 0.2544 REMARK 3 10 1.9166 - 1.8505 0.95 2537 147 0.2469 0.2892 REMARK 3 11 1.8505 - 1.7927 0.95 2581 144 0.2672 0.2756 REMARK 3 12 1.7927 - 1.7415 0.95 2550 142 0.2980 0.3577 REMARK 3 13 1.7415 - 1.6957 0.92 2501 135 0.3840 0.3810 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.10 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: 0.3200 REMARK 3 OPERATOR: -H,L,K REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2692 REMARK 3 ANGLE : 1.015 3679 REMARK 3 CHIRALITY : 0.054 386 REMARK 3 PLANARITY : 0.006 467 REMARK 3 DIHEDRAL : 19.046 1519 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 22.8678 0.3310 17.7790 REMARK 3 T TENSOR REMARK 3 T11: 0.1545 T22: 0.1439 REMARK 3 T33: 0.1845 T12: -0.0014 REMARK 3 T13: -0.0196 T23: -0.0182 REMARK 3 L TENSOR REMARK 3 L11: 0.7446 L22: 0.3038 REMARK 3 L33: 0.1422 L12: -0.3260 REMARK 3 L13: -0.1350 L23: -0.0923 REMARK 3 S TENSOR REMARK 3 S11: 0.0024 S12: -0.0024 S13: 0.0338 REMARK 3 S21: -0.0110 S22: -0.0177 S23: -0.0451 REMARK 3 S31: -0.0061 S32: 0.0130 S33: 0.0146 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 6VSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000246998. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-17 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 : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.48 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35767 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 46.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.95700 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: PHASER REMARK 200 STARTING MODEL: 1DF7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE, 100 MM MES (2 REMARK 280 -(N-MORPHOLINO) ETHANESULFONIC ACID), PH 6.5, 10 MM COCL2, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 297K 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 30.87250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.89900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.58550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.89900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.87250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.58550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 MET A -1 REMARK 465 THR A 0 REMARK 465 MET B -1 REMARK 465 THR B 0 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 B 141 CG CD OE1 OE2 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 390 O HOH B 422 2.00 REMARK 500 O HOH B 435 O HOH B 437 2.04 REMARK 500 O HOH B 396 O HOH B 411 2.04 REMARK 500 O HOH A 401 O HOH A 433 2.05 REMARK 500 O PHE A 144 O HOH A 301 2.07 REMARK 500 O HOH B 380 O HOH B 417 2.07 REMARK 500 O HOH B 352 O HOH B 383 2.08 REMARK 500 O HOH A 326 O HOH A 445 2.09 REMARK 500 O HOH A 353 O HOH A 370 2.10 REMARK 500 O HOH B 334 O HOH B 386 2.10 REMARK 500 O HOH B 430 O HOH B 432 2.12 REMARK 500 O HOH A 392 O HOH A 443 2.13 REMARK 500 O HOH B 367 O HOH B 404 2.14 REMARK 500 O HOH B 404 O HOH B 416 2.15 REMARK 500 O HOH A 365 O HOH A 435 2.16 REMARK 500 O1 SO4 A 204 O HOH A 302 2.16 REMARK 500 OE1 GLU A 122 O HOH A 303 2.17 REMARK 500 O HOH B 338 O HOH B 430 2.17 REMARK 500 O HOH B 353 O HOH B 411 2.17 REMARK 500 O HOH B 344 O HOH B 348 2.18 REMARK 500 O HOH A 411 O HOH A 453 2.18 REMARK 500 OE1 GLN B 68 O HOH B 301 2.18 REMARK 500 O HOH A 426 O HOH B 313 2.18 REMARK 500 NH2 ARG B 143 O HOH B 302 2.18 REMARK 500 O HOH B 331 O HOH B 364 2.19 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 356 O HOH B 437 3655 2.09 REMARK 500 O HOH A 315 O HOH A 380 3545 2.15 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 ASP A 19 -159.04 -133.19 REMARK 500 PRO A 21 35.27 -82.68 REMARK 500 LEU A 86 61.32 -100.05 REMARK 500 ASP A 116 66.59 -68.33 REMARK 500 ASP A 132 -163.46 -79.66 REMARK 500 PRO B 21 37.20 -77.01 REMARK 500 ASP B 132 -154.02 -77.88 REMARK 500 ARG B 146 1.59 -66.64 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 470 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A 471 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A 472 DISTANCE = 7.20 ANGSTROMS REMARK 525 HOH A 473 DISTANCE = 8.44 ANGSTROMS REMARK 525 HOH B 437 DISTANCE = 6.52 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 CO A 203 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 38 NE2 REMARK 620 2 HOH A 343 O 88.3 REMARK 620 3 HOH A 344 O 91.8 172.6 REMARK 620 4 HOH A 350 O 89.4 104.5 82.9 REMARK 620 5 HOH A 375 O 88.3 86.1 86.4 169.0 REMARK 620 6 HIS B 157 NE2 169.2 82.9 97.8 86.9 97.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 203 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 38 NE2 REMARK 620 2 HOH B 315 O 87.2 REMARK 620 3 HOH B 325 O 96.8 86.3 REMARK 620 4 HOH B 341 O 87.5 173.9 97.5 REMARK 620 5 HOH B 381 O 96.9 93.0 166.3 84.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JBB A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JBB B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 204 DBREF 6VSD A -1 159 UNP P9WNX1 DYR_MYCTU 1 161 DBREF 6VSD B -1 159 UNP P9WNX1 DYR_MYCTU 1 161 SEQRES 1 A 161 MET THR MET VAL GLY LEU ILE TRP ALA GLN ALA THR SER SEQRES 2 A 161 GLY VAL ILE GLY ARG GLY GLY ASP ILE PRO TRP ARG LEU SEQRES 3 A 161 PRO GLU ASP GLN ALA HIS PHE ARG GLU ILE THR MET GLY SEQRES 4 A 161 HIS THR ILE VAL MET GLY ARG ARG THR TRP ASP SER LEU SEQRES 5 A 161 PRO ALA LYS VAL ARG PRO LEU PRO GLY ARG ARG ASN VAL SEQRES 6 A 161 VAL LEU SER ARG GLN ALA ASP PHE MET ALA SER GLY ALA SEQRES 7 A 161 GLU VAL VAL GLY SER LEU GLU GLU ALA LEU THR SER PRO SEQRES 8 A 161 GLU THR TRP VAL ILE GLY GLY GLY GLN VAL TYR ALA LEU SEQRES 9 A 161 ALA LEU PRO TYR ALA THR ARG CYS GLU VAL THR GLU VAL SEQRES 10 A 161 ASP ILE GLY LEU PRO ARG GLU ALA GLY ASP ALA LEU ALA SEQRES 11 A 161 PRO VAL LEU ASP GLU THR TRP ARG GLY GLU THR GLY GLU SEQRES 12 A 161 TRP ARG PHE SER ARG SER GLY LEU ARG TYR ARG LEU TYR SEQRES 13 A 161 SER TYR HIS ARG SER SEQRES 1 B 161 MET THR MET VAL GLY LEU ILE TRP ALA GLN ALA THR SER SEQRES 2 B 161 GLY VAL ILE GLY ARG GLY GLY ASP ILE PRO TRP ARG LEU SEQRES 3 B 161 PRO GLU ASP GLN ALA HIS PHE ARG GLU ILE THR MET GLY SEQRES 4 B 161 HIS THR ILE VAL MET GLY ARG ARG THR TRP ASP SER LEU SEQRES 5 B 161 PRO ALA LYS VAL ARG PRO LEU PRO GLY ARG ARG ASN VAL SEQRES 6 B 161 VAL LEU SER ARG GLN ALA ASP PHE MET ALA SER GLY ALA SEQRES 7 B 161 GLU VAL VAL GLY SER LEU GLU GLU ALA LEU THR SER PRO SEQRES 8 B 161 GLU THR TRP VAL ILE GLY GLY GLY GLN VAL TYR ALA LEU SEQRES 9 B 161 ALA LEU PRO TYR ALA THR ARG CYS GLU VAL THR GLU VAL SEQRES 10 B 161 ASP ILE GLY LEU PRO ARG GLU ALA GLY ASP ALA LEU ALA SEQRES 11 B 161 PRO VAL LEU ASP GLU THR TRP ARG GLY GLU THR GLY GLU SEQRES 12 B 161 TRP ARG PHE SER ARG SER GLY LEU ARG TYR ARG LEU TYR SEQRES 13 B 161 SER TYR HIS ARG SER HET JBB A 201 16 HET NAP A 202 48 HET CO A 203 1 HET SO4 A 204 5 HET JBB B 201 16 HET NAP B 202 48 HET CO B 203 1 HET PO4 B 204 5 HETNAM JBB 3-(THIOPHEN-2-YLSULFANYLMETHYL)BENZOIC ACID HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM CO COBALT (II) ION HETNAM SO4 SULFATE ION HETNAM PO4 PHOSPHATE ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 JBB 2(C12 H10 O2 S2) FORMUL 4 NAP 2(C21 H28 N7 O17 P3) FORMUL 5 CO 2(CO 2+) FORMUL 6 SO4 O4 S 2- FORMUL 10 PO4 O4 P 3- FORMUL 11 HOH *310(H2 O) HELIX 1 AA1 LEU A 24 MET A 36 1 13 HELIX 2 AA2 ARG A 44 LEU A 50 1 7 HELIX 3 AA3 LEU A 82 LEU A 86 5 5 HELIX 4 AA4 GLY A 96 LEU A 104 1 9 HELIX 5 AA5 PRO A 105 ALA A 107 5 3 HELIX 6 AA6 LEU B 24 MET B 36 1 13 HELIX 7 AA7 ARG B 44 LEU B 50 1 7 HELIX 8 AA8 PRO B 51 ARG B 55 5 5 HELIX 9 AA9 SER B 81 LEU B 86 1 6 HELIX 10 AB1 GLY B 96 LEU B 104 1 9 HELIX 11 AB2 PRO B 105 ALA B 107 5 3 SHEET 1 AA1 8 GLU A 77 VAL A 79 0 SHEET 2 AA1 8 ARG A 61 LEU A 65 1 N VAL A 64 O GLU A 77 SHEET 3 AA1 8 THR A 39 GLY A 43 1 N MET A 42 O LEU A 65 SHEET 4 AA1 8 THR A 91 VAL A 93 1 O TRP A 92 N THR A 39 SHEET 5 AA1 8 VAL A 2 ALA A 9 1 N GLY A 3 O VAL A 93 SHEET 6 AA1 8 ARG A 109 VAL A 115 1 O VAL A 115 N GLN A 8 SHEET 7 AA1 8 ARG A 150 HIS A 157 -1 O TYR A 154 N VAL A 112 SHEET 8 AA1 8 ARG A 136 GLU A 138 -1 N ARG A 136 O HIS A 157 SHEET 1 AA2 8 GLU A 77 VAL A 79 0 SHEET 2 AA2 8 ARG A 61 LEU A 65 1 N VAL A 64 O GLU A 77 SHEET 3 AA2 8 THR A 39 GLY A 43 1 N MET A 42 O LEU A 65 SHEET 4 AA2 8 THR A 91 VAL A 93 1 O TRP A 92 N THR A 39 SHEET 5 AA2 8 VAL A 2 ALA A 9 1 N GLY A 3 O VAL A 93 SHEET 6 AA2 8 ARG A 109 VAL A 115 1 O VAL A 115 N GLN A 8 SHEET 7 AA2 8 ARG A 150 HIS A 157 -1 O TYR A 154 N VAL A 112 SHEET 8 AA2 8 ARG A 143 PHE A 144 -1 N ARG A 143 O TYR A 151 SHEET 1 AA3 2 VAL A 13 GLY A 15 0 SHEET 2 AA3 2 ALA A 126 LEU A 127 -1 O ALA A 126 N ILE A 14 SHEET 1 AA4 8 GLU B 77 VAL B 79 0 SHEET 2 AA4 8 ARG B 61 LEU B 65 1 N VAL B 64 O GLU B 77 SHEET 3 AA4 8 THR B 39 GLY B 43 1 N ILE B 40 O ARG B 61 SHEET 4 AA4 8 THR B 91 GLY B 95 1 O TRP B 92 N THR B 39 SHEET 5 AA4 8 VAL B 2 ALA B 9 1 N GLY B 3 O THR B 91 SHEET 6 AA4 8 ARG B 109 VAL B 115 1 O GLU B 111 N LEU B 4 SHEET 7 AA4 8 ARG B 150 HIS B 157 -1 O TYR B 154 N VAL B 112 SHEET 8 AA4 8 ARG B 136 THR B 139 -1 N ARG B 136 O HIS B 157 SHEET 1 AA5 8 GLU B 77 VAL B 79 0 SHEET 2 AA5 8 ARG B 61 LEU B 65 1 N VAL B 64 O GLU B 77 SHEET 3 AA5 8 THR B 39 GLY B 43 1 N ILE B 40 O ARG B 61 SHEET 4 AA5 8 THR B 91 GLY B 95 1 O TRP B 92 N THR B 39 SHEET 5 AA5 8 VAL B 2 ALA B 9 1 N GLY B 3 O THR B 91 SHEET 6 AA5 8 ARG B 109 VAL B 115 1 O GLU B 111 N LEU B 4 SHEET 7 AA5 8 ARG B 150 HIS B 157 -1 O TYR B 154 N VAL B 112 SHEET 8 AA5 8 ARG B 143 PHE B 144 -1 N ARG B 143 O TYR B 151 SHEET 1 AA6 2 VAL B 13 GLY B 15 0 SHEET 2 AA6 2 ALA B 126 LEU B 127 -1 O ALA B 126 N ILE B 14 LINK NE2 HIS A 38 CO CO A 203 1555 1555 2.22 LINK CO CO A 203 O HOH A 343 1555 1555 2.18 LINK CO CO A 203 O HOH A 344 1555 1555 1.94 LINK CO CO A 203 O HOH A 350 1555 1555 2.25 LINK CO CO A 203 O HOH A 375 1555 1555 1.87 LINK CO CO A 203 NE2 HIS B 157 1555 1555 2.02 LINK NE2 HIS B 38 CO CO B 203 1555 1555 2.03 LINK CO CO B 203 O HOH B 315 1555 1555 2.50 LINK CO CO B 203 O HOH B 325 1555 1555 2.22 LINK CO CO B 203 O HOH B 341 1555 1555 2.26 LINK CO CO B 203 O HOH B 381 1555 1555 2.01 CISPEP 1 ARG A 55 PRO A 56 0 0.32 CISPEP 2 GLY A 95 GLY A 96 0 0.22 CISPEP 3 ARG B 55 PRO B 56 0 -4.68 CISPEP 4 GLY B 95 GLY B 96 0 -1.07 SITE 1 AC1 5 ARG A 23 LEU A 50 VAL A 54 ILE A 94 SITE 2 AC1 5 NAP A 202 SITE 1 AC2 33 TRP A 6 ALA A 7 ILE A 14 GLY A 15 SITE 2 AC2 33 GLY A 18 ASP A 19 ILE A 20 GLY A 43 SITE 3 AC2 33 ARG A 44 ARG A 45 THR A 46 LEU A 65 SITE 4 AC2 33 SER A 66 ARG A 67 GLN A 68 GLY A 80 SITE 5 AC2 33 ILE A 94 GLY A 95 GLY A 96 GLY A 97 SITE 6 AC2 33 GLN A 98 VAL A 99 TYR A 100 LEU A 102 SITE 7 AC2 33 JBB A 201 HOH A 302 HOH A 314 HOH A 333 SITE 8 AC2 33 HOH A 338 HOH A 352 HOH A 357 HOH A 382 SITE 9 AC2 33 HOH A 394 SITE 1 AC3 6 HIS A 38 HOH A 343 HOH A 344 HOH A 350 SITE 2 AC3 6 HOH A 375 HIS B 157 SITE 1 AC4 4 ARG A 44 ARG A 45 HOH A 302 HOH A 313 SITE 1 AC5 6 GLN B 28 PHE B 31 ARG B 32 LEU B 50 SITE 2 AC5 6 ARG B 60 NAP B 202 SITE 1 AC6 32 TRP B 6 ALA B 7 ILE B 14 GLY B 15 SITE 2 AC6 32 ARG B 16 GLY B 18 ASP B 19 ILE B 20 SITE 3 AC6 32 GLY B 43 ARG B 44 ARG B 45 THR B 46 SITE 4 AC6 32 LEU B 65 SER B 66 ARG B 67 GLN B 68 SITE 5 AC6 32 GLY B 80 ILE B 94 GLY B 96 GLY B 97 SITE 6 AC6 32 GLN B 98 VAL B 99 TYR B 100 LEU B 102 SITE 7 AC6 32 JBB B 201 HOH B 304 HOH B 319 HOH B 334 SITE 8 AC6 32 HOH B 343 HOH B 344 HOH B 348 HOH B 353 SITE 1 AC7 6 HIS A 157 HIS B 38 HOH B 315 HOH B 325 SITE 2 AC7 6 HOH B 341 HOH B 381 SITE 1 AC8 4 ARG A 23 HOH A 389 HOH A 399 ARG B 32 CRYST1 61.745 71.171 71.798 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 0.016196 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014051 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013928 0.00000