HEADER OXIDOREDUCTASE 22-FEB-16 5IBI TITLE CRYSTAL STRUCTURE MYCOBACTERIUM TUBERCULOSIS CYP121 IN COMPLEX WITH TITLE 2 INHIBITOR FRAGMENT 26A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 121 CYP121; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: P450 HEME-THIOLATE PROTEIN CYP121; COMPND 5 EC: 1.14.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: CYP121, CYP121_1, EI32_2700, ERS007657_00455, ERS007661_00083, SOURCE 5 ERS007663_02869, ERS007665_01035, ERS007670_00377, ERS007672_00334, SOURCE 6 ERS007679_00173, ERS007681_01277, ERS007703_02339, ERS007720_01219, SOURCE 7 ERS007722_01069, ERS013447_00077, ERS013471_02812, ERS023446_00317, SOURCE 8 ERS024276_01833, ERS027644_00398, ERS027652_00994, ERS027654_01464, SOURCE 9 ERS027656_01022, ERS027659_00311, ERS027666_00100, ERS031537_01827, SOURCE 10 ERS075357_02976, ERS075361_02508, ERS075387_01689, ERS124361_02646, SOURCE 11 HX90_2763; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MYCOBACTERIUM TUBERCULOSIS CYP121 FRAGMENT BASED INHIBITOR SCREENING, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.LEVY REVDAT 2 27-APR-16 5IBI 1 JRNL REVDAT 1 06-APR-16 5IBI 0 JRNL AUTH M.E.KAVANAGH,A.G.COYNE,K.J.MCLEAN,G.G.JAMES,C.W.LEVY, JRNL AUTH 2 L.B.MARINO,L.P.DE CARVALHO,D.S.CHAN,S.A.HUDSON,S.SURADE, JRNL AUTH 3 D.LEYS,A.W.MUNRO,C.ABELL JRNL TITL FRAGMENT-BASED APPROACHES TO THE DEVELOPMENT OF JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS CYP121 INHIBITORS. JRNL REF J.MED.CHEM. V. 59 3272 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 27002486 JRNL DOI 10.1021/ACS.JMEDCHEM.6B00007 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 45602 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.980 REMARK 3 FREE R VALUE TEST SET COUNT : 3641 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 47.2646 - 6.5108 1.00 1614 132 0.1617 0.1701 REMARK 3 2 6.5108 - 5.1699 1.00 1621 137 0.1785 0.2300 REMARK 3 3 5.1699 - 4.5170 1.00 1625 146 0.1462 0.1887 REMARK 3 4 4.5170 - 4.1042 1.00 1592 143 0.1397 0.1434 REMARK 3 5 4.1042 - 3.8102 1.00 1633 140 0.1540 0.1905 REMARK 3 6 3.8102 - 3.5856 1.00 1610 145 0.1585 0.1830 REMARK 3 7 3.5856 - 3.4061 1.00 1602 142 0.1702 0.2036 REMARK 3 8 3.4061 - 3.2579 1.00 1614 139 0.1877 0.2010 REMARK 3 9 3.2579 - 3.1325 1.00 1614 145 0.1997 0.2676 REMARK 3 10 3.1325 - 3.0244 1.00 1611 143 0.2128 0.2469 REMARK 3 11 3.0244 - 2.9299 1.00 1622 140 0.2117 0.2261 REMARK 3 12 2.9299 - 2.8461 1.00 1624 143 0.2169 0.2372 REMARK 3 13 2.8461 - 2.7712 1.00 1600 137 0.2160 0.2476 REMARK 3 14 2.7712 - 2.7036 1.00 1620 130 0.2112 0.2306 REMARK 3 15 2.7036 - 2.6422 1.00 1603 142 0.2276 0.2969 REMARK 3 16 2.6422 - 2.5859 1.00 1607 140 0.2226 0.2590 REMARK 3 17 2.5859 - 2.5342 1.00 1634 142 0.2216 0.2838 REMARK 3 18 2.5342 - 2.4864 1.00 1614 142 0.2182 0.2866 REMARK 3 19 2.4864 - 2.4420 1.00 1589 138 0.2274 0.3081 REMARK 3 20 2.4420 - 2.4006 1.00 1647 137 0.2287 0.2744 REMARK 3 21 2.4006 - 2.3619 1.00 1584 134 0.2244 0.2989 REMARK 3 22 2.3619 - 2.3255 1.00 1653 142 0.2190 0.2391 REMARK 3 23 2.3255 - 2.2913 1.00 1577 139 0.2264 0.2605 REMARK 3 24 2.2913 - 2.2591 1.00 1646 148 0.2172 0.2702 REMARK 3 25 2.2591 - 2.2285 1.00 1586 137 0.2318 0.2965 REMARK 3 26 2.2285 - 2.1996 0.98 1619 138 0.2225 0.2900 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 3217 REMARK 3 ANGLE : 1.037 4399 REMARK 3 CHIRALITY : 0.035 499 REMARK 3 PLANARITY : 0.007 567 REMARK 3 DIHEDRAL : 13.008 1198 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 5IBI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218572. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 - 6.15 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45602 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 47.254 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.16150 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : 0.28240 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.300 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: INHOUSE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5-2.1 M AMMONIUM SULFATE AND 0.1 M REMARK 280 SODIUM MES OR CACODYLATE FROM PH 5.5-6.1, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K 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 176.72533 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 88.36267 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 132.54400 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 44.18133 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 220.90667 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 176.72533 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 88.36267 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 44.18133 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 132.54400 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 220.90667 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL 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 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 A 597 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 826 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 892 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 930 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 MET A 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 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 A 17 NE CZ NH1 NH2 REMARK 470 GLU A 24 CD OE1 OE2 REMARK 470 ARG A 162 CG CD NE CZ NH1 NH2 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 PHE A 168 O HOH A 501 2.11 REMARK 500 O THR A 103 O HOH A 502 2.16 REMARK 500 O HOH A 702 O HOH A 794 2.18 REMARK 500 O HOH A 711 O HOH A 871 2.18 REMARK 500 N GLN A 385 O HOH A 501 2.18 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 573 O HOH A 822 10555 2.16 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 ARG A 28 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 28 NE - CZ - NH2 ANGL. DEV. = 3.2 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 GLU A 29 75.29 -155.22 REMARK 500 ASN A 84 35.92 -99.05 REMARK 500 PHE A 137 -71.34 -140.91 REMARK 500 ARG A 340 144.54 -171.71 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 933 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 934 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A 935 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A 936 DISTANCE = 6.67 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 HEM A 405 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 512 O REMARK 620 2 HEM A 405 NA 96.2 REMARK 620 3 HEM A 405 NB 90.2 90.0 REMARK 620 4 HEM A 405 NC 83.5 178.4 88.4 REMARK 620 5 HEM A 405 ND 92.6 90.3 177.2 91.3 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 SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 69U A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 405 DBREF1 5IBI A 1 396 UNP A0A0T9WNE5_MYCTX DBREF2 5IBI A A0A0T9WNE5 1 396 SEQRES 1 A 396 MET THR ALA THR VAL LEU LEU GLU VAL PRO PHE SER ALA SEQRES 2 A 396 ARG GLY ASP ARG ILE PRO ASP ALA VAL ALA GLU LEU ARG SEQRES 3 A 396 THR ARG GLU PRO ILE ARG LYS VAL ARG THR ILE THR GLY SEQRES 4 A 396 ALA GLU ALA TRP LEU VAL SER SER TYR ALA LEU CYS THR SEQRES 5 A 396 GLN VAL LEU GLU ASP ARG ARG PHE SER MET LYS GLU THR SEQRES 6 A 396 ALA ALA ALA GLY ALA PRO ARG LEU ASN ALA LEU THR VAL SEQRES 7 A 396 PRO PRO GLU VAL VAL ASN ASN MET GLY ASN ILE ALA ASP SEQRES 8 A 396 ALA GLY LEU ARG LYS ALA VAL MET LYS ALA ILE THR PRO SEQRES 9 A 396 LYS ALA PRO GLY LEU GLU GLN PHE LEU ARG ASP THR ALA SEQRES 10 A 396 ASN SER LEU LEU ASP ASN LEU ILE THR GLU GLY ALA PRO SEQRES 11 A 396 ALA ASP LEU ARG ASN ASP PHE ALA ASP PRO LEU ALA THR SEQRES 12 A 396 ALA LEU HIS CYS LYS VAL LEU GLY ILE PRO GLN GLU ASP SEQRES 13 A 396 GLY PRO LYS LEU PHE ARG SER LEU SER ILE ALA PHE MET SEQRES 14 A 396 SER SER ALA ASP PRO ILE PRO ALA ALA LYS ILE ASN TRP SEQRES 15 A 396 ASP ARG ASP ILE GLU TYR MET ALA GLY ILE LEU GLU ASN SEQRES 16 A 396 PRO ASN ILE THR THR GLY LEU MET GLY GLU LEU SER ARG SEQRES 17 A 396 LEU ARG LYS ASP PRO ALA TYR SER HIS VAL SER ASP GLU SEQRES 18 A 396 LEU PHE ALA THR ILE GLY VAL THR PHE PHE GLY ALA GLY SEQRES 19 A 396 VAL ILE SER THR GLY SER PHE LEU THR THR ALA LEU ILE SEQRES 20 A 396 SER LEU ILE GLN ARG PRO GLN LEU ARG ASN LEU LEU HIS SEQRES 21 A 396 GLU LYS PRO GLU LEU ILE PRO ALA GLY VAL GLU GLU LEU SEQRES 22 A 396 LEU ARG ILE ASN LEU SER PHE ALA ASP GLY LEU PRO ARG SEQRES 23 A 396 LEU ALA THR ALA ASP ILE GLN VAL GLY ASP VAL LEU VAL SEQRES 24 A 396 ARG LYS GLY GLU LEU VAL LEU VAL LEU LEU GLU GLY ALA SEQRES 25 A 396 ASN PHE ASP PRO GLU HIS PHE PRO ASN PRO GLY SER ILE SEQRES 26 A 396 GLU LEU ASP ARG PRO ASN PRO THR SER HIS LEU ALA PHE SEQRES 27 A 396 GLY ARG GLY GLN HIS PHE CYS PRO GLY SER ALA LEU GLY SEQRES 28 A 396 ARG ARG HIS ALA GLN ILE GLY ILE GLU ALA LEU LEU LYS SEQRES 29 A 396 LYS MET PRO GLY VAL ASP LEU ALA VAL PRO ILE ASP GLN SEQRES 30 A 396 LEU VAL TRP ARG THR ARG PHE GLN ARG ARG ILE PRO GLU SEQRES 31 A 396 ARG LEU PRO VAL LEU TRP HET SO4 A 401 5 HET SO4 A 402 5 HET SO4 A 403 5 HET 69U A 404 28 HET HEM A 405 43 HETNAM SO4 SULFATE ION HETNAM 69U 4,4'-(5-{[(4-HYDROXYPHENYL)METHYL]AMINO}-1H-PYRAZOLE-3, HETNAM 2 69U 4-DIYL)DIPHENOL HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 69U C22 H19 N3 O3 FORMUL 6 HEM C34 H32 FE N4 O4 FORMUL 7 HOH *436(H2 O) HELIX 1 AA1 PRO A 19 GLU A 29 1 11 HELIX 2 AA2 SER A 47 GLU A 56 1 10 HELIX 3 AA3 MET A 62 ALA A 67 5 6 HELIX 4 AA4 PRO A 79 VAL A 83 5 5 HELIX 5 AA5 ASN A 84 GLY A 93 1 10 HELIX 6 AA6 LEU A 94 ILE A 102 1 9 HELIX 7 AA7 GLY A 108 GLY A 128 1 21 HELIX 8 AA8 PHE A 137 GLY A 151 1 15 HELIX 9 AA9 PRO A 153 GLU A 155 5 3 HELIX 10 AB1 ASP A 156 ARG A 162 1 7 HELIX 11 AB2 SER A 163 PHE A 168 1 6 HELIX 12 AB3 ILE A 175 ASN A 195 1 21 HELIX 13 AB4 THR A 200 LYS A 211 1 12 HELIX 14 AB5 ASP A 212 SER A 216 5 5 HELIX 15 AB6 SER A 219 GLN A 251 1 33 HELIX 16 AB7 ARG A 252 LYS A 262 1 11 HELIX 17 AB8 LEU A 265 ILE A 276 1 12 HELIX 18 AB9 LEU A 308 PHE A 314 1 7 HELIX 19 AC1 ARG A 340 PHE A 344 5 5 HELIX 20 AC2 GLY A 347 MET A 366 1 20 HELIX 21 AC3 PRO A 374 LEU A 378 5 5 SHEET 1 AA1 5 ILE A 31 ARG A 35 0 SHEET 2 AA1 5 GLU A 41 VAL A 45 -1 O LEU A 44 N ARG A 32 SHEET 3 AA1 5 LEU A 304 VAL A 307 1 O LEU A 306 N TRP A 43 SHEET 4 AA1 5 LEU A 284 ALA A 288 -1 N ARG A 286 O VAL A 305 SHEET 5 AA1 5 PHE A 60 SER A 61 -1 N SER A 61 O LEU A 287 SHEET 1 AA2 3 ALA A 131 ASP A 132 0 SHEET 2 AA2 3 PRO A 393 LEU A 395 -1 O VAL A 394 N ALA A 131 SHEET 3 AA2 3 ASP A 370 LEU A 371 -1 N ASP A 370 O LEU A 395 SHEET 1 AA3 2 ILE A 292 VAL A 294 0 SHEET 2 AA3 2 VAL A 297 VAL A 299 -1 O VAL A 297 N VAL A 294 LINK FE HEM A 405 O HOH A 512 1555 1555 2.65 CISPEP 1 VAL A 9 PRO A 10 0 -0.42 CISPEP 2 ALA A 129 PRO A 130 0 2.47 SITE 1 AC1 7 LYS A 211 PRO A 330 ASN A 331 PRO A 332 SITE 2 AC1 7 THR A 333 SER A 334 HOH A 602 SITE 1 AC2 8 SER A 12 ARG A 14 HOH A 521 HOH A 531 SITE 2 AC2 8 HOH A 582 HOH A 644 HOH A 690 HOH A 773 SITE 1 AC3 7 ARG A 58 SER A 61 MET A 62 LYS A 63 SITE 2 AC3 7 HIS A 343 HOH A 513 HOH A 529 SITE 1 AC4 15 THR A 65 ARG A 72 LEU A 76 THR A 77 SITE 2 AC4 15 VAL A 78 ASN A 85 ALA A 167 PHE A 168 SITE 3 AC4 15 TRP A 182 VAL A 228 GLN A 385 HEM A 405 SITE 4 AC4 15 HOH A 525 HOH A 657 HOH A 696 SITE 1 AC5 21 MET A 62 MET A 86 HIS A 146 GLY A 234 SITE 2 AC5 21 SER A 237 PHE A 241 PHE A 280 LEU A 284 SITE 3 AC5 21 ARG A 286 ALA A 337 PHE A 338 GLY A 339 SITE 4 AC5 21 HIS A 343 CYS A 345 69U A 404 HOH A 512 SITE 5 AC5 21 HOH A 574 HOH A 630 HOH A 637 HOH A 657 SITE 6 AC5 21 HOH A 685 CRYST1 77.822 77.822 265.088 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 0.012850 0.007419 0.000000 0.00000 SCALE2 0.000000 0.014838 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003772 0.00000