HEADER OXIDOREDUCTASE 14-JUL-16 5LI8
TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYP126A1 IN COMPLEX
TITLE 2 WITH KETOCONAZOLE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PUTATIVE CYTOCHROME P450 126;
COMPND 3 CHAIN: A;
COMPND 4 EC: 1.14.-.-;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN CDC 1551 /
SOURCE 3 OSHKOSH);
SOURCE 4 ORGANISM_TAXID: 83331;
SOURCE 5 GENE: CYP126, MT0802;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS MONOXYGENASE, CYTOCHROME P450, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.LEVY,A.W.MUNRO,D.LEYS
REVDAT 3 10-JAN-24 5LI8 1 REMARK
REVDAT 2 06-DEC-17 5LI8 1 JRNL
REVDAT 1 21-DEC-16 5LI8 0
JRNL AUTH J.T.CHENGE,L.V.DUYET,S.SWAMI,K.J.MCLEAN,M.E.KAVANAGH,
JRNL AUTH 2 A.G.COYNE,S.E.RIGBY,M.R.CHEESMAN,H.M.GIRVAN,C.W.LEVY,B.RUPP,
JRNL AUTH 3 J.P.VON KRIES,C.ABELL,D.LEYS,A.W.MUNRO
JRNL TITL STRUCTURAL CHARACTERIZATION AND LIGAND/INHIBITOR
JRNL TITL 2 IDENTIFICATION PROVIDE FUNCTIONAL INSIGHTS INTO THE
JRNL TITL 3 MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP126A1.
JRNL REF J. BIOL. CHEM. V. 292 1310 2017
JRNL REFN ESSN 1083-351X
JRNL PMID 27932461
JRNL DOI 10.1074/JBC.M116.748822
REMARK 2
REMARK 2 RESOLUTION. 1.83 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.86
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 37753
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) : 0.157
REMARK 3 R VALUE (WORKING SET) : 0.155
REMARK 3 FREE R VALUE : 0.196
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1996
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) : 1.83
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1746
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.2400
REMARK 3 BIN FREE R VALUE SET COUNT : 84
REMARK 3 BIN FREE R VALUE : 0.3350
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3031
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 79
REMARK 3 SOLVENT ATOMS : 484
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.97
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.11000
REMARK 3 B22 (A**2) : 0.03000
REMARK 3 B33 (A**2) : -0.10000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.42000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.115
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.335
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3252 ; 0.025 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 2195 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4451 ; 2.001 ; 2.016
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5292 ; 1.082 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 398 ; 5.534 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 149 ;28.138 ;22.550
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 495 ;12.256 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;19.381 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 484 ; 0.127 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3661 ; 0.003 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 690 ; 0.000 ; 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): 1978 ; 1.232 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 795 ; 0.413 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3191 ; 2.122 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1274 ; 3.476 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1260 ; 5.471 ; 4.500
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): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
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 : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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 5LI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUL-16.
REMARK 100 THE DEPOSITION ID IS D_1200000787.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 29-JAN-10
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 : 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) : 0.976
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37754
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830
REMARK 200 RESOLUTION RANGE LOW (A) : 43.860
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5
REMARK 200 DATA REDUNDANCY : 3.900
REMARK 200 R MERGE (I) : 0.04800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88
REMARK 200 COMPLETENESS FOR SHELL (%) : 59.1
REMARK 200 DATA REDUNDANCY IN SHELL : 3.30
REMARK 200 R MERGE FOR SHELL (I) : 0.66600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: 1OXA
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.98
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M SODIUM SULPHATE, 0.1 M TRIS, PH
REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 59.11500
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.83000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.11500
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.83000
REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1250 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 16320 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 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 THR A 3
REMARK 465 ALA A 4
REMARK 465 ALA A 5
REMARK 465 GLY A 75
REMARK 465 GLY A 76
REMARK 465 GLN A 77
REMARK 465 ARG A 78
REMARK 465 ARG A 79
REMARK 465 GLY A 179
REMARK 465 PHE A 180
REMARK 465 ASP A 181
REMARK 465 PHE A 182
REMARK 465 ARG A 183
REMARK 465 GLY A 184
REMARK 465 SER A 185
REMARK 465 ARG A 186
REMARK 465 ARG A 187
REMARK 465 ALA A 188
REMARK 465 THR A 189
REMARK 465 MET A 190
REMARK 465 PRO A 191
REMARK 465 ARG A 192
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 GLN A 86 CG CD OE1 NE2
REMARK 470 ARG A 117 CG CD NE CZ NH1 NH2
REMARK 470 ARG A 120 CZ NH1 NH2
REMARK 470 GLU A 174 CG CD OE1 OE2
REMARK 470 LEU A 193 CG CD1 CD2
REMARK 470 GLU A 196 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 A 866 O HOH A 867 1.09
REMARK 500 O HOH A 623 O HOH A 929 1.15
REMARK 500 O HOH A 617 O HOH A 850 1.16
REMARK 500 O HOH A 708 O HOH A 738 1.16
REMARK 500 O HOH A 771 O HOH A 805 1.19
REMARK 500 O HOH A 609 O HOH A 747 1.27
REMARK 500 O HOH A 937 O HOH A 975 1.31
REMARK 500 O HOH A 732 O HOH A 777 1.33
REMARK 500 O HOH A 601 O HOH A 717 1.38
REMARK 500 O HOH A 604 O HOH A 871 1.56
REMARK 500 O HOH A 928 O HOH A 973 1.58
REMARK 500 O HOH A 630 O HOH A 804 1.72
REMARK 500 O TYR A 70 O HOH A 601 1.74
REMARK 500 O HOH A 607 O HOH A 773 1.81
REMARK 500 OD1 ASP A 274 O HOH A 602 1.85
REMARK 500 O HOH A 798 O HOH A 1023 1.85
REMARK 500 O HOH A 826 O HOH A 1017 1.85
REMARK 500 O HOH A 851 O HOH A 1023 1.86
REMARK 500 OD1 ASP A 100 OG1 THR A 104 1.95
REMARK 500 O HOH A 609 O HOH A 874 2.01
REMARK 500 CB ASP A 339 O HOH A 934 2.03
REMARK 500 O HOH A 611 O HOH A 955 2.09
REMARK 500 O HOH A 798 O HOH A 851 2.10
REMARK 500 O HOH A 957 O HOH A 991 2.16
REMARK 500 CE2 TYR A 37 O HOH A 985 2.17
REMARK 500 CB ARG A 121 O HOH A 606 2.17
REMARK 500 O HOH A 751 O HOH A 904 2.19
REMARK 500 O HOH A 803 O HOH A 1068 2.19
REMARK 500 NH1 ARG A 340 O HOH A 603 2.19
REMARK 500 O HOH A 729 O HOH A 1010 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 854 O HOH A 854 2555 1.69
REMARK 500 O HOH A 795 O HOH A 937 4445 1.87
REMARK 500 O HOH A 739 O HOH A 854 2555 1.90
REMARK 500 O HOH A 625 O HOH A 739 2555 2.06
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 SER A 312 CB SER A 312 OG -0.082
REMARK 500 ARG A 370 CD ARG A 370 NE -0.136
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 65 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 ASP A 100 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 ASP A 100 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES
REMARK 500 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 ARG A 121 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 ARG A 127 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 ARG A 259 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 ARG A 259 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 ARG A 370 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 ARG A 370 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES
REMARK 500 ARG A 374 NE - CZ - NH1 ANGL. DEV. = 3.6 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 34 90.87 -163.46
REMARK 500 ILE A 149 -53.77 -134.41
REMARK 500 ALA A 235 56.71 -142.50
REMARK 500 ASP A 282 89.82 -159.33
REMARK 500 SER A 298 67.74 31.21
REMARK 500 GLN A 358 140.16 -171.81
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 A1083 DISTANCE = 6.00 ANGSTROMS
REMARK 525 HOH A1084 DISTANCE = 7.06 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 363 SG
REMARK 620 2 HEM A 501 NA 95.0
REMARK 620 3 HEM A 501 NB 85.7 91.3
REMARK 620 4 HEM A 501 NC 86.1 178.9 88.7
REMARK 620 5 HEM A 501 ND 93.4 90.1 178.4 89.9
REMARK 620 6 KKK A 502 N2 171.3 90.8 87.7 88.1 93.0
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 KKK A 502
DBREF 5LI8 A 1 414 UNP P9WPN8 CP126_MYCTO 1 414
SEQRES 1 A 414 MET THR THR ALA ALA GLY LEU SER GLY ILE ASP LEU THR
SEQRES 2 A 414 ASP LEU ASP ASN PHE ALA ASP GLY PHE PRO HIS HIS LEU
SEQRES 3 A 414 PHE ALA ILE HIS ARG ARG GLU ALA PRO VAL TYR TRP HIS
SEQRES 4 A 414 ARG PRO THR GLU HIS THR PRO ASP GLY GLU GLY PHE TRP
SEQRES 5 A 414 SER VAL ALA THR TYR ALA GLU THR LEU GLU VAL LEU ARG
SEQRES 6 A 414 ASP PRO VAL THR TYR SER SER VAL THR GLY GLY GLN ARG
SEQRES 7 A 414 ARG PHE GLY GLY THR VAL LEU GLN ASP LEU PRO VAL ALA
SEQRES 8 A 414 GLY GLN VAL LEU ASN MET MET ASP ASP PRO ARG HIS THR
SEQRES 9 A 414 ARG ILE ARG ARG LEU VAL SER SER GLY LEU THR PRO ARG
SEQRES 10 A 414 MET ILE ARG ARG VAL GLU ASP ASP LEU ARG ARG ARG ALA
SEQRES 11 A 414 ARG GLY LEU LEU ASP GLY VAL GLU PRO GLY ALA PRO PHE
SEQRES 12 A 414 ASP PHE VAL VAL GLU ILE ALA ALA GLU LEU PRO MET GLN
SEQRES 13 A 414 MET ILE CYS ILE LEU LEU GLY VAL PRO GLU THR ASP ARG
SEQRES 14 A 414 HIS TRP LEU PHE GLU ALA VAL GLU PRO GLY PHE ASP PHE
SEQRES 15 A 414 ARG GLY SER ARG ARG ALA THR MET PRO ARG LEU ASN VAL
SEQRES 16 A 414 GLU ASP ALA GLY SER ARG LEU TYR THR TYR ALA LEU GLU
SEQRES 17 A 414 LEU ILE ALA GLY LYS ARG ALA GLU PRO ALA ASP ASP MET
SEQRES 18 A 414 LEU SER VAL VAL ALA ASN ALA THR ILE ASP ASP PRO ASP
SEQRES 19 A 414 ALA PRO ALA LEU SER ASP ALA GLU LEU TYR LEU PHE PHE
SEQRES 20 A 414 HIS LEU LEU PHE SER ALA GLY ALA GLU THR THR ARG ASN
SEQRES 21 A 414 SER ILE ALA GLY GLY LEU LEU ALA LEU ALA GLU ASN PRO
SEQRES 22 A 414 ASP GLN LEU GLN THR LEU ARG SER ASP PHE GLU LEU LEU
SEQRES 23 A 414 PRO THR ALA ILE GLU GLU ILE VAL ARG TRP THR SER PRO
SEQRES 24 A 414 SER PRO SER LYS ARG ARG THR ALA SER ARG ALA VAL SER
SEQRES 25 A 414 LEU GLY GLY GLN PRO ILE GLU ALA GLY GLN LYS VAL VAL
SEQRES 26 A 414 VAL TRP GLU GLY SER ALA ASN ARG ASP PRO SER VAL PHE
SEQRES 27 A 414 ASP ARG ALA ASP GLU PHE ASP ILE THR ARG LYS PRO ASN
SEQRES 28 A 414 PRO HIS LEU GLY PHE GLY GLN GLY VAL HIS TYR CYS LEU
SEQRES 29 A 414 GLY ALA ASN LEU ALA ARG LEU GLU LEU ARG VAL LEU PHE
SEQRES 30 A 414 GLU GLU LEU LEU SER ARG PHE GLY SER VAL ARG VAL VAL
SEQRES 31 A 414 GLU PRO ALA GLU TRP THR ARG SER ASN ARG HIS THR GLY
SEQRES 32 A 414 ILE ARG HIS LEU VAL VAL GLU LEU ARG GLY GLY
HET HEM A 501 43
HET KKK A 502 36
HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE
HETNAM KKK 1-ACETYL-4-(4-{[(2R,4S)-2-(2,4-DICHLOROPHENYL)-2-(1H-
HETNAM 2 KKK IMIDAZOL-1-YLMETHYL)-1,3-DIOXOLAN-4-
HETNAM 3 KKK YL]METHOXY}PHENYL)PIPERAZINE
HETSYN HEM HEME
FORMUL 2 HEM C34 H32 FE N4 O4
FORMUL 3 KKK C26 H28 CL2 N4 O4
FORMUL 4 HOH *484(H2 O)
HELIX 1 AA1 GLY A 6 ILE A 10 5 5
HELIX 2 AA2 ASP A 14 PHE A 18 5 5
HELIX 3 AA3 PRO A 23 ALA A 34 1 12
HELIX 4 AA4 THR A 45 GLU A 49 5 5
HELIX 5 AA5 THR A 56 ARG A 65 1 10
HELIX 6 AA6 VAL A 94 MET A 98 5 5
HELIX 7 AA7 PRO A 101 LEU A 114 1 14
HELIX 8 AA8 THR A 115 GLY A 136 1 22
HELIX 9 AA9 PHE A 145 ILE A 149 1 5
HELIX 10 AB1 ALA A 151 LEU A 162 1 12
HELIX 11 AB2 PRO A 165 THR A 167 5 3
HELIX 12 AB3 ASP A 168 GLU A 177 1 10
HELIX 13 AB4 ASN A 194 GLU A 216 1 23
HELIX 14 AB5 ASP A 220 ASN A 227 1 8
HELIX 15 AB6 SER A 239 ASN A 272 1 34
HELIX 16 AB7 ASN A 272 SER A 281 1 10
HELIX 17 AB8 ASP A 282 GLU A 284 5 3
HELIX 18 AB9 LEU A 285 SER A 298 1 14
HELIX 19 AC1 TRP A 327 ASN A 332 1 6
HELIX 20 AC2 GLY A 365 PHE A 384 1 20
SHEET 1 AA1 5 VAL A 36 HIS A 39 0
SHEET 2 AA1 5 PHE A 51 VAL A 54 -1 O PHE A 51 N HIS A 39
SHEET 3 AA1 5 LYS A 323 VAL A 326 1 O VAL A 325 N TRP A 52
SHEET 4 AA1 5 LYS A 303 ALA A 307 -1 N ARG A 305 O VAL A 324
SHEET 5 AA1 5 TYR A 70 SER A 71 -1 N SER A 71 O THR A 306
SHEET 1 AA2 3 PHE A 143 ASP A 144 0
SHEET 2 AA2 3 VAL A 408 ARG A 412 -1 O VAL A 409 N PHE A 143
SHEET 3 AA2 3 SER A 386 VAL A 389 -1 N ARG A 388 O GLU A 410
SHEET 1 AA3 2 VAL A 311 LEU A 313 0
SHEET 2 AA3 2 GLN A 316 ILE A 318 -1 O ILE A 318 N VAL A 311
SHEET 1 AA4 2 GLU A 394 TRP A 395 0
SHEET 2 AA4 2 ILE A 404 HIS A 406 -1 O ARG A 405 N GLU A 394
LINK SG CYS A 363 FE HEM A 501 1555 1555 2.32
LINK FE HEM A 501 N2 KKK A 502 1555 1555 2.00
CISPEP 1 ASP A 100 PRO A 101 0 6.73
CISPEP 2 LYS A 349 PRO A 350 0 -0.07
SITE 1 AC1 20 LEU A 95 ASN A 96 HIS A 103 ARG A 107
SITE 2 AC1 20 THR A 257 THR A 258 LYS A 303 ARG A 305
SITE 3 AC1 20 GLY A 355 PHE A 356 GLY A 357 HIS A 361
SITE 4 AC1 20 CYS A 363 GLY A 365 ALA A 369 KKK A 502
SITE 5 AC1 20 HOH A 617 HOH A 651 HOH A 749 HOH A 850
SITE 1 AC2 12 THR A 13 PRO A 46 VAL A 94 ASN A 96
SITE 2 AC2 12 PHE A 246 ALA A 253 SER A 302 ASN A 399
SITE 3 AC2 12 ARG A 400 HEM A 501 HOH A 876 HOH A 977
CRYST1 118.230 59.660 69.840 90.00 93.21 90.00 C 1 2 1 4
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 0.008458 0.000000 0.000474 0.00000
SCALE2 0.000000 0.016762 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014341 0.00000