HEADER OXIDOREDUCTASE 05-JAN-16 5HDI TITLE STRUCTURAL CHARACTERIZATION OF CYP144A1, A MYCOBACTERIUM TUBERCULOSIS TITLE 2 CYTOCHROME P450 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 144; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.14.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: CYP144, RV1777, MTCY25C11.04; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MONOOXYGENASE, CYTOCHROME P450, HEME-BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.CHENGE,M.D.DRISCOLL,K.J.MCLEAN,A.W.MUNRO,D.LEYS REVDAT 3 10-JAN-24 5HDI 1 LINK REVDAT 2 08-JUN-16 5HDI 1 JRNL REVDAT 1 04-MAY-16 5HDI 0 JRNL AUTH J.CHENGE,M.E.KAVANAGH,M.D.DRISCOLL,K.J.MCLEAN,D.B.YOUNG, JRNL AUTH 2 T.CORTES,D.MATAK-VINKOVIC,C.W.LEVY,S.E.RIGBY,D.LEYS,C.ABELL, JRNL AUTH 3 A.W.MUNRO JRNL TITL STRUCTURAL CHARACTERIZATION OF CYP144A1 - A CYTOCHROME P450 JRNL TITL 2 ENZYME EXPRESSED FROM ALTERNATIVE TRANSCRIPTS IN JRNL TITL 3 MYCOBACTERIUM TUBERCULOSIS. JRNL REF SCI REP V. 6 26628 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27225995 JRNL DOI 10.1038/SREP26628 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 84.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 116903 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6118 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8401 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE SET COUNT : 441 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6044 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 546 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.01000 REMARK 3 B22 (A**2) : -2.08000 REMARK 3 B33 (A**2) : 0.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.076 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.320 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6469 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6129 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8866 ; 1.872 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14016 ; 0.987 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 832 ; 5.672 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 289 ;36.219 ;23.149 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1002 ;12.953 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 58 ;18.530 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 983 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7554 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1544 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 12598 ; 7.629 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 128 ;26.910 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 12851 ;17.578 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5HDI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216834. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 116903 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 88.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.80700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: 2XKR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLOGRAPHY WAS PERFORMED USING REMARK 280 THE SITTING DROP METHOD USING 20 MG/ML CYP144A1. DROPS WERE REMARK 280 PREPARED BY THE ADDITION OF 0.2 MICROL OF CYP144A1-FLV AND -TRV REMARK 280 PROTEINS TO 0.2 MICROL OF MOTHER LIQUOR AND BY INCUBATING AT 4 REMARK 280 OC. FOLLOWING INITIAL CRYSTALLOGENESIS USING COMMERCIAL SCREENS, REMARK 280 CRYSTALLIZATION CONDITIONS WERE FURTHER REFINED TO 0.8 OR 1.0 M REMARK 280 (NH4)2SO4 WITH 0.1 M HEPES, PH 7.55, AND 25% PEG 3350. SINGLE REMARK 280 CRYSTALS WERE FLASH COOLED AFTER ADDITION OF 10% PEG 200 AS REMARK 280 CRYOPROTECTANT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 29.17500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.04500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.89500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.04500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.17500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.89500 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 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 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 32 REMARK 465 THR A 33 REMARK 465 ILE A 34 REMARK 465 ALA A 35 REMARK 465 LYS A 36 REMARK 465 GLY A 372 REMARK 465 GLY A 373 REMARK 465 MET B 32 REMARK 465 THR B 33 REMARK 465 ILE B 34 REMARK 465 ALA B 35 REMARK 465 LYS B 36 REMARK 465 ASP B 37 REMARK 465 ALA B 38 REMARK 465 ASN B 39 REMARK 465 ALA B 371 REMARK 465 GLY B 372 REMARK 465 GLY B 373 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 ASP A 37 CG OD1 OD2 REMARK 470 GLU A 103 CG CD OE1 OE2 REMARK 470 LYS A 374 CG CD CE NZ REMARK 470 ARG B 146 CD NE CZ NH1 NH2 REMARK 470 ASP B 192 CB CG OD1 OD2 REMARK 470 LYS B 374 CG CD CE NZ 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 621 O HOH B 709 0.62 REMARK 500 SG CYS B 168 O HOH B 832 0.97 REMARK 500 O HOH B 652 O HOH B 704 1.41 REMARK 500 CB CYS B 168 O HOH B 832 1.94 REMARK 500 O HOH B 638 O HOH B 821 2.08 REMARK 500 CG2 THR A 262 O HOH A 792 2.09 REMARK 500 O HOH B 652 O HOH B 765 2.11 REMARK 500 CB CYS B 168 O HOH B 832 2.12 REMARK 500 OG1 THR B 40 O HOH B 601 2.14 REMARK 500 OE2 GLU A 88 O HOH A 601 2.18 REMARK 500 O MET B 98 O HOH B 602 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 B 610 O HOH B 853 4456 0.97 REMARK 500 OG1 THR B 334 O HOH B 748 4456 2.18 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 ASP A 112 CB ASP A 112 CG 0.131 REMARK 500 LYS A 374 C LYS A 374 O -0.117 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 58 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 86 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP A 216 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 294 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 327 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG B 133 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 MET B 148 CG - SD - CE ANGL. DEV. = -15.7 DEGREES REMARK 500 ASP B 216 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG B 294 CD - NE - CZ ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG B 294 NE - CZ - NH1 ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG B 294 NE - CZ - NH2 ANGL. DEV. = -9.0 DEGREES REMARK 500 ARG B 327 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ASP B 343 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG B 393 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 401 NE - CZ - NH2 ANGL. DEV. = -5.1 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 ALA A 67 -129.48 51.84 REMARK 500 MET A 111 -143.75 -123.96 REMARK 500 LEU A 121 -108.40 50.23 REMARK 500 MET A 175 -66.36 -130.53 REMARK 500 ASP A 242 81.63 -156.87 REMARK 500 THR A 333 -165.49 -160.06 REMARK 500 THR A 333 -168.14 -160.06 REMARK 500 LYS A 381 146.80 -170.03 REMARK 500 MET B 111 -147.22 -125.35 REMARK 500 LEU B 121 -106.48 57.17 REMARK 500 LEU B 121 -106.48 57.18 REMARK 500 MET B 175 -68.52 -133.95 REMARK 500 ASP B 192 61.20 39.29 REMARK 500 ASP B 242 73.47 -157.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 HIS B 139 0.06 SIDE CHAIN 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 880 DISTANCE = 9.38 ANGSTROMS REMARK 525 HOH B 866 DISTANCE = 5.93 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 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 386 SG REMARK 620 2 HEM A 501 NA 96.7 REMARK 620 3 HEM A 501 NB 86.8 91.9 REMARK 620 4 HEM A 501 NC 86.2 177.1 88.0 REMARK 620 5 HEM A 501 ND 96.4 88.3 176.8 91.7 REMARK 620 6 HOH A 615 O 175.8 82.0 89.3 95.2 87.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 386 SG REMARK 620 2 HEM B 501 NA 96.1 REMARK 620 3 HEM B 501 NB 88.1 91.7 REMARK 620 4 HEM B 501 NC 87.3 176.5 87.7 REMARK 620 5 HEM B 501 ND 95.8 88.3 176.1 92.1 REMARK 620 6 HOH B 620 O 175.4 81.4 88.1 95.2 88.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 501 DBREF 5HDI A 32 435 UNP P9WPL1 CP144_MYCTU 31 434 DBREF 5HDI B 32 435 UNP P9WPL1 CP144_MYCTU 31 434 SEQRES 1 A 404 MET THR ILE ALA LYS ASP ALA ASN THR PHE PHE GLY ALA SEQRES 2 A 404 GLU SER VAL GLN ASP PRO TYR PRO LEU TYR GLU ARG MET SEQRES 3 A 404 ARG ALA ALA GLY SER VAL HIS ARG ILE ALA ASN SER ASP SEQRES 4 A 404 PHE TYR ALA VAL CYS GLY TRP ASP ALA VAL ASN GLU ALA SEQRES 5 A 404 ILE GLY ARG PRO GLU ASP PHE SER SER ASN LEU THR ALA SEQRES 6 A 404 THR MET THR TYR THR ALA GLU GLY THR ALA LYS PRO PHE SEQRES 7 A 404 GLU MET ASP PRO LEU GLY GLY PRO THR HIS VAL LEU ALA SEQRES 8 A 404 THR ALA ASP ASP PRO ALA HIS ALA VAL HIS ARG LYS LEU SEQRES 9 A 404 VAL LEU ARG HIS LEU ALA ALA LYS ARG ILE ARG VAL MET SEQRES 10 A 404 GLU GLN PHE THR VAL GLN ALA ALA ASP ARG LEU TRP VAL SEQRES 11 A 404 ASP GLY MET GLN ASP GLY CYS ILE GLU TRP MET GLY ALA SEQRES 12 A 404 MET ALA ASN ARG LEU PRO MET MET VAL VAL ALA GLU LEU SEQRES 13 A 404 ILE GLY LEU PRO ASP PRO ASP ILE ALA GLN LEU VAL LYS SEQRES 14 A 404 TRP GLY TYR ALA ALA THR GLN LEU LEU GLU GLY LEU VAL SEQRES 15 A 404 GLU ASN ASP GLN LEU VAL ALA ALA GLY VAL ALA LEU MET SEQRES 16 A 404 GLU LEU SER GLY TYR ILE PHE GLU GLN PHE ASP ARG ALA SEQRES 17 A 404 ALA ALA ASP PRO ARG ASP ASN LEU LEU GLY GLU LEU ALA SEQRES 18 A 404 THR ALA CYS ALA SER GLY GLU LEU ASP THR LEU THR ALA SEQRES 19 A 404 GLN VAL MET MET VAL THR LEU PHE ALA ALA GLY GLY GLU SEQRES 20 A 404 SER THR ALA ALA LEU LEU GLY SER ALA VAL TRP ILE LEU SEQRES 21 A 404 ALA THR ARG PRO ASP ILE GLN GLN GLN VAL ARG ALA ASN SEQRES 22 A 404 PRO GLU LEU LEU GLY ALA PHE ILE GLU GLU THR LEU ARG SEQRES 23 A 404 TYR GLU PRO PRO PHE ARG GLY HIS TYR ARG HIS VAL ARG SEQRES 24 A 404 ASN ALA THR THR LEU ASP GLY THR GLU LEU PRO ALA ASP SEQRES 25 A 404 SER HIS LEU LEU LEU LEU TRP GLY ALA ALA ASN ARG ASP SEQRES 26 A 404 PRO ALA GLN PHE GLU ALA PRO GLY GLU PHE ARG LEU ASP SEQRES 27 A 404 ARG ALA GLY GLY LYS GLY HIS ILE SER PHE GLY LYS GLY SEQRES 28 A 404 ALA HIS PHE CYS VAL GLY ALA ALA LEU ALA ARG LEU GLU SEQRES 29 A 404 ALA ARG ILE VAL LEU ARG LEU LEU LEU ASP ARG THR SER SEQRES 30 A 404 VAL ILE GLU ALA ALA ASP VAL GLY GLY TRP LEU PRO SER SEQRES 31 A 404 ILE LEU VAL ARG ARG ILE GLU ARG LEU GLU LEU ALA VAL SEQRES 32 A 404 GLN SEQRES 1 B 404 MET THR ILE ALA LYS ASP ALA ASN THR PHE PHE GLY ALA SEQRES 2 B 404 GLU SER VAL GLN ASP PRO TYR PRO LEU TYR GLU ARG MET SEQRES 3 B 404 ARG ALA ALA GLY SER VAL HIS ARG ILE ALA ASN SER ASP SEQRES 4 B 404 PHE TYR ALA VAL CYS GLY TRP ASP ALA VAL ASN GLU ALA SEQRES 5 B 404 ILE GLY ARG PRO GLU ASP PHE SER SER ASN LEU THR ALA SEQRES 6 B 404 THR MET THR TYR THR ALA GLU GLY THR ALA LYS PRO PHE SEQRES 7 B 404 GLU MET ASP PRO LEU GLY GLY PRO THR HIS VAL LEU ALA SEQRES 8 B 404 THR ALA ASP ASP PRO ALA HIS ALA VAL HIS ARG LYS LEU SEQRES 9 B 404 VAL LEU ARG HIS LEU ALA ALA LYS ARG ILE ARG VAL MET SEQRES 10 B 404 GLU GLN PHE THR VAL GLN ALA ALA ASP ARG LEU TRP VAL SEQRES 11 B 404 ASP GLY MET GLN ASP GLY CYS ILE GLU TRP MET GLY ALA SEQRES 12 B 404 MET ALA ASN ARG LEU PRO MET MET VAL VAL ALA GLU LEU SEQRES 13 B 404 ILE GLY LEU PRO ASP PRO ASP ILE ALA GLN LEU VAL LYS SEQRES 14 B 404 TRP GLY TYR ALA ALA THR GLN LEU LEU GLU GLY LEU VAL SEQRES 15 B 404 GLU ASN ASP GLN LEU VAL ALA ALA GLY VAL ALA LEU MET SEQRES 16 B 404 GLU LEU SER GLY TYR ILE PHE GLU GLN PHE ASP ARG ALA SEQRES 17 B 404 ALA ALA ASP PRO ARG ASP ASN LEU LEU GLY GLU LEU ALA SEQRES 18 B 404 THR ALA CYS ALA SER GLY GLU LEU ASP THR LEU THR ALA SEQRES 19 B 404 GLN VAL MET MET VAL THR LEU PHE ALA ALA GLY GLY GLU SEQRES 20 B 404 SER THR ALA ALA LEU LEU GLY SER ALA VAL TRP ILE LEU SEQRES 21 B 404 ALA THR ARG PRO ASP ILE GLN GLN GLN VAL ARG ALA ASN SEQRES 22 B 404 PRO GLU LEU LEU GLY ALA PHE ILE GLU GLU THR LEU ARG SEQRES 23 B 404 TYR GLU PRO PRO PHE ARG GLY HIS TYR ARG HIS VAL ARG SEQRES 24 B 404 ASN ALA THR THR LEU ASP GLY THR GLU LEU PRO ALA ASP SEQRES 25 B 404 SER HIS LEU LEU LEU LEU TRP GLY ALA ALA ASN ARG ASP SEQRES 26 B 404 PRO ALA GLN PHE GLU ALA PRO GLY GLU PHE ARG LEU ASP SEQRES 27 B 404 ARG ALA GLY GLY LYS GLY HIS ILE SER PHE GLY LYS GLY SEQRES 28 B 404 ALA HIS PHE CYS VAL GLY ALA ALA LEU ALA ARG LEU GLU SEQRES 29 B 404 ALA ARG ILE VAL LEU ARG LEU LEU LEU ASP ARG THR SER SEQRES 30 B 404 VAL ILE GLU ALA ALA ASP VAL GLY GLY TRP LEU PRO SER SEQRES 31 B 404 ILE LEU VAL ARG ARG ILE GLU ARG LEU GLU LEU ALA VAL SEQRES 32 B 404 GLN HET HEM A 501 43 HET HEM B 501 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *546(H2 O) HELIX 1 AA1 GLY A 43 ASP A 49 1 7 HELIX 2 AA2 PRO A 50 GLY A 61 1 12 HELIX 3 AA3 GLY A 76 GLY A 85 1 10 HELIX 4 AA4 VAL A 120 ALA A 124 5 5 HELIX 5 AA5 PRO A 127 ARG A 138 1 12 HELIX 6 AA6 ALA A 141 MET A 164 1 24 HELIX 7 AA7 TRP A 171 MET A 175 1 5 HELIX 8 AA8 ARG A 178 GLY A 189 1 12 HELIX 9 AA9 ASP A 194 TYR A 203 1 10 HELIX 10 AB1 TYR A 203 GLY A 211 1 9 HELIX 11 AB2 GLU A 214 ASP A 242 1 29 HELIX 12 AB3 ASN A 246 SER A 257 1 12 HELIX 13 AB4 ASP A 261 GLY A 277 1 17 HELIX 14 AB5 GLY A 277 ARG A 294 1 18 HELIX 15 AB6 ARG A 294 ASN A 304 1 11 HELIX 16 AB7 LEU A 307 GLU A 319 1 13 HELIX 17 AB8 LEU A 349 ASN A 354 1 6 HELIX 18 AB9 LYS A 381 PHE A 385 5 5 HELIX 19 AC1 GLY A 388 ARG A 406 1 19 HELIX 20 AC2 GLY B 43 ASP B 49 1 7 HELIX 21 AC3 PRO B 50 GLY B 61 1 12 HELIX 22 AC4 GLY B 76 GLY B 85 1 10 HELIX 23 AC5 VAL B 120 ALA B 124 5 5 HELIX 24 AC6 PRO B 127 ARG B 138 1 12 HELIX 25 AC7 ALA B 141 MET B 164 1 24 HELIX 26 AC8 TRP B 171 MET B 175 1 5 HELIX 27 AC9 ARG B 178 GLY B 189 1 12 HELIX 28 AD1 ASP B 194 GLY B 211 1 18 HELIX 29 AD2 GLU B 214 ASP B 242 1 29 HELIX 30 AD3 ASN B 246 SER B 257 1 12 HELIX 31 AD4 ASP B 261 GLY B 277 1 17 HELIX 32 AD5 GLY B 277 ARG B 294 1 18 HELIX 33 AD6 ARG B 294 ASN B 304 1 11 HELIX 34 AD7 LEU B 307 GLU B 319 1 13 HELIX 35 AD8 LEU B 349 ASN B 354 1 6 HELIX 36 AD9 LYS B 381 PHE B 385 5 5 HELIX 37 AE1 GLY B 388 THR B 407 1 20 SHEET 1 AA1 5 VAL A 63 ARG A 65 0 SHEET 2 AA1 5 PHE A 71 VAL A 74 -1 O ALA A 73 N HIS A 64 SHEET 3 AA1 5 HIS A 345 LEU A 348 1 O LEU A 347 N VAL A 74 SHEET 4 AA1 5 HIS A 325 VAL A 329 -1 N HIS A 325 O LEU A 348 SHEET 5 AA1 5 PHE A 90 SER A 91 -1 N SER A 91 O HIS A 328 SHEET 1 AA2 2 ALA A 96 TYR A 100 0 SHEET 2 AA2 2 ALA A 106 GLU A 110 -1 O PHE A 109 N THR A 97 SHEET 1 AA3 3 CYS A 168 GLU A 170 0 SHEET 2 AA3 3 LEU A 430 GLN A 435 -1 O LEU A 432 N ILE A 169 SHEET 3 AA3 3 VAL A 409 VAL A 415 -1 N ALA A 413 O GLU A 431 SHEET 1 AA4 2 THR A 333 LEU A 335 0 SHEET 2 AA4 2 THR A 338 LEU A 340 -1 O LEU A 340 N THR A 333 SHEET 1 AA5 5 VAL B 63 ARG B 65 0 SHEET 2 AA5 5 PHE B 71 VAL B 74 -1 O ALA B 73 N HIS B 64 SHEET 3 AA5 5 HIS B 345 LEU B 348 1 O LEU B 347 N VAL B 74 SHEET 4 AA5 5 HIS B 325 VAL B 329 -1 N HIS B 325 O LEU B 348 SHEET 5 AA5 5 PHE B 90 SER B 91 -1 N SER B 91 O HIS B 328 SHEET 1 AA6 2 ALA B 96 TYR B 100 0 SHEET 2 AA6 2 ALA B 106 GLU B 110 -1 O PHE B 109 N THR B 97 SHEET 1 AA7 3 CYS B 168 GLU B 170 0 SHEET 2 AA7 3 LEU B 430 GLN B 435 -1 O LEU B 432 N ILE B 169 SHEET 3 AA7 3 VAL B 409 VAL B 415 -1 N ASP B 414 O GLU B 431 SHEET 1 AA8 2 THR B 333 LEU B 335 0 SHEET 2 AA8 2 THR B 338 LEU B 340 -1 O LEU B 340 N THR B 333 LINK SG CYS A 386 FE HEM A 501 1555 1555 2.32 LINK FE HEM A 501 O HOH A 615 1555 1555 2.39 LINK SG CYS B 386 FE HEM B 501 1555 1555 2.32 LINK FE HEM B 501 O HOH B 620 1555 1555 2.47 CISPEP 1 ASP A 126 PRO A 127 0 3.78 CISPEP 2 ASP B 126 PRO B 127 0 4.89 SITE 1 AC1 24 LEU A 121 ALA A 122 HIS A 129 ARG A 133 SITE 2 AC1 24 ALA A 275 GLY A 276 SER A 279 THR A 280 SITE 3 AC1 24 PHE A 322 HIS A 325 ARG A 327 SER A 378 SITE 4 AC1 24 PHE A 379 GLY A 380 ALA A 383 HIS A 384 SITE 5 AC1 24 CYS A 386 VAL A 387 GLY A 388 ALA A 392 SITE 6 AC1 24 HOH A 615 HOH A 628 HOH A 680 HOH A 681 SITE 1 AC2 24 LEU B 121 ALA B 122 HIS B 129 ARG B 133 SITE 2 AC2 24 ALA B 275 GLY B 276 SER B 279 THR B 280 SITE 3 AC2 24 PHE B 322 HIS B 325 ARG B 327 SER B 378 SITE 4 AC2 24 PHE B 379 GLY B 380 ALA B 383 HIS B 384 SITE 5 AC2 24 CYS B 386 VAL B 387 GLY B 388 ALA B 392 SITE 6 AC2 24 HOH B 620 HOH B 631 HOH B 687 HOH B 693 CRYST1 58.350 117.790 122.090 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 0.017138 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008490 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008191 0.00000