HEADER OXIDOREDUCTASE 19-SEP-08 3EKD TITLE CRYSTAL STRUCTURE OF THE A264M HEME DOMAIN OF CYTOCHROME P450 BM3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450(BM-3); COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HEME DOMAIN; COMPND 5 SYNONYM: P450BM-3, CYTOCHROME P450 102, NADPH--CYTOCHROME P450 COMPND 6 REDUCTASE; COMPND 7 EC: 1.14.14.1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS MEGATERIUM; SOURCE 3 ORGANISM_TAXID: 1404; SOURCE 4 GENE: CYP102A1, CYP102; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEME LIGATION, CYTOCHROME P450, CYTOPLASM, ELECTRON TRANSPORT, FAD, KEYWDS 2 FLAVOPROTEIN, FMN, HEME, IRON, METAL-BINDING, MONOOXYGENASE, KEYWDS 3 MULTIFUNCTIONAL ENZYME, NADP, OXIDOREDUCTASE, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR H.S.TOOGOOD,D.LEYS REVDAT 3 30-AUG-23 3EKD 1 REMARK REVDAT 2 20-OCT-21 3EKD 1 REMARK SEQADV REVDAT 1 30-DEC-08 3EKD 0 JRNL AUTH H.M.GIRVAN,H.S.TOOGOOD,R.E.LITTLEFORD,H.E.SEWARD,W.E.SMITH, JRNL AUTH 2 I.S.EKANEM,D.LEYS,M.R.CHEESMAN,A.W.MUNRO JRNL TITL NOVEL HAEM CO-ORDINATION VARIANTS OF FLAVOCYTOCHROME JRNL TITL 2 P450BM3. JRNL REF BIOCHEM.J. V. 417 65 2009 JRNL REFN ISSN 0264-6021 JRNL PMID 18721129 JRNL DOI 10.1042/BJ20081133 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 40923 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2179 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2946 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 168 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7247 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 104 REMARK 3 SOLVENT ATOMS : 172 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : 0.85000 REMARK 3 B33 (A**2) : -1.26000 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): 0.460 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.275 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.204 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.357 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7532 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 5150 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10218 ; 2.002 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12571 ; 1.265 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 905 ; 6.657 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 356 ;37.782 ;24.663 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1300 ;17.112 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;16.441 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1097 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8301 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1461 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1238 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3824 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2992 ; 0.165 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2778 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 100 ; 0.139 ; 0.200 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): 8 ; 0.078 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 22 ; 0.213 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.037 ; 0.200 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): 5695 ; 1.054 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1812 ; 0.158 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7331 ; 1.308 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3365 ; 2.054 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2883 ; 2.950 ; 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 : 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 3EKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000049431. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40923 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: 2IJ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUMSULPHATE AND PEG, PH 6.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 31.88450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.97150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 62.58550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.97150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.88450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 62.58550 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 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A 227 REMARK 465 GLU A 228 REMARK 465 GLN A 229 REMARK 465 ILE A 458 REMARK 465 PRO A 459 REMARK 465 SER A 460 REMARK 465 PRO A 461 REMARK 465 SER A 462 REMARK 465 THR A 463 REMARK 465 GLU A 464 REMARK 465 GLN A 465 REMARK 465 SER A 466 REMARK 465 ALA A 467 REMARK 465 LYS A 468 REMARK 465 LYS A 469 REMARK 465 VAL A 470 REMARK 465 THR B 1 REMARK 465 GLY B 227 REMARK 465 GLU B 228 REMARK 465 PRO B 459 REMARK 465 SER B 460 REMARK 465 PRO B 461 REMARK 465 SER B 462 REMARK 465 THR B 463 REMARK 465 GLU B 464 REMARK 465 GLN B 465 REMARK 465 SER B 466 REMARK 465 ALA B 467 REMARK 465 LYS B 468 REMARK 465 LYS B 469 REMARK 465 VAL B 470 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 4 CG CD OE1 OE2 REMARK 470 LYS A 31 CE NZ REMARK 470 LYS A 94 CE NZ REMARK 470 GLN A 109 CG CD OE1 NE2 REMARK 470 GLN A 110 CD OE1 NE2 REMARK 470 LYS A 113 CD CE NZ REMARK 470 ASN A 192 CG OD1 ND2 REMARK 470 LYS A 210 CE NZ REMARK 470 LYS A 218 CG CD CE NZ REMARK 470 LYS A 224 CD CE NZ REMARK 470 GLN A 288 CD OE1 NE2 REMARK 470 LYS A 306 CD CE NZ REMARK 470 LYS B 3 CD CE NZ REMARK 470 GLU B 4 CG CD OE1 OE2 REMARK 470 LYS B 9 CG CD CE NZ REMARK 470 LYS B 15 CE NZ REMARK 470 LYS B 41 CE NZ REMARK 470 LYS B 59 CE NZ REMARK 470 ASP B 136 CG OD1 OD2 REMARK 470 GLN B 189 CG CD OE1 NE2 REMARK 470 ASN B 192 CG OD1 ND2 REMARK 470 ASP B 199 CG OD1 OD2 REMARK 470 LYS B 202 CG CD CE NZ REMARK 470 GLN B 229 CG CD OE1 NE2 REMARK 470 LYS B 241 CD CE NZ REMARK 470 LYS B 306 CG CD CE NZ 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 TRP A 130 CB TRP A 130 CG 0.124 REMARK 500 GLU B 352 CD GLU B 352 OE1 0.068 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 LEU A 20 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 68 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 432 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 132 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 132 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP B 338 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 PRO B 382 C - N - CA ANGL. DEV. = 11.1 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 LYS A 15 -136.67 54.44 REMARK 500 ASP A 84 47.76 -109.48 REMARK 500 ASP A 136 0.12 -64.86 REMARK 500 ASP A 195 152.45 -48.96 REMARK 500 ILE A 263 -74.57 -72.21 REMARK 500 HIS A 266 -36.89 -138.47 REMARK 500 GLU A 344 -17.22 -140.09 REMARK 500 LYS A 349 116.75 -34.83 REMARK 500 SER A 383 81.95 -56.24 REMARK 500 ALA A 384 29.56 153.51 REMARK 500 HIS A 388 19.22 80.93 REMARK 500 LEU A 437 -70.13 80.76 REMARK 500 MET B 5 135.20 -34.40 REMARK 500 PRO B 8 15.37 -68.57 REMARK 500 LYS B 9 154.15 60.35 REMARK 500 LYS B 15 -156.07 56.20 REMARK 500 ASN B 16 2.54 -62.55 REMARK 500 LEU B 20 44.82 -95.67 REMARK 500 ASN B 21 59.37 -102.13 REMARK 500 ARG B 47 144.76 -173.17 REMARK 500 ASP B 84 36.74 -84.53 REMARK 500 ASP B 195 119.31 -26.78 REMARK 500 TYR B 198 31.60 -66.70 REMARK 500 LYS B 224 0.09 -59.17 REMARK 500 SER B 230 144.71 38.11 REMARK 500 ASP B 231 54.11 -117.28 REMARK 500 GLU B 244 -61.56 -153.78 REMARK 500 ASP B 250 153.69 -49.46 REMARK 500 HIS B 266 -36.46 -148.66 REMARK 500 ASP B 370 42.60 -80.91 REMARK 500 ARG B 375 81.58 -150.48 REMARK 500 ARG B 378 -33.54 -31.19 REMARK 500 PRO B 382 -56.35 -27.56 REMARK 500 THR B 436 51.33 -149.68 REMARK 500 LEU B 437 -56.36 67.96 REMARK 500 REMARK 500 REMARK: NULL 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 472 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 400 SG REMARK 620 2 HEM A 472 NA 93.1 REMARK 620 3 HEM A 472 NB 92.0 97.8 REMARK 620 4 HEM A 472 NC 90.0 175.4 85.5 REMARK 620 5 HEM A 472 ND 91.2 84.4 176.0 92.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 471 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 400 SG REMARK 620 2 HEM B 471 NA 94.5 REMARK 620 3 HEM B 471 NB 80.6 90.0 REMARK 620 4 HEM B 471 NC 83.2 177.7 89.6 REMARK 620 5 HEM B 471 ND 92.7 90.7 173.4 89.4 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 PAM A 471 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 472 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 471 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EKF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A264Q MUTANT REMARK 900 RELATED ID: 3EKB RELATED DB: PDB REMARK 900 STRUCTURE OF THE A264C MUTANT REMARK 900 RELATED ID: 1SMI RELATED DB: PDB REMARK 900 STRUCTURE OF THE A264E MUTANT REMARK 900 RELATED ID: 2IJ3 RELATED DB: PDB REMARK 900 STRUCTURE OF THE A264H MUTANT REMARK 900 RELATED ID: 2IJ4 RELATED DB: PDB REMARK 900 STRUCTURE OF THE A264K MUTANT DBREF 3EKD A 1 470 UNP P14779 CPXB_BACME 2 471 DBREF 3EKD B 1 470 UNP P14779 CPXB_BACME 2 471 SEQADV 3EKD MET A 264 UNP P14779 ALA 265 ENGINEERED MUTATION SEQADV 3EKD MET B 264 UNP P14779 ALA 265 ENGINEERED MUTATION SEQRES 1 A 470 THR ILE LYS GLU MET PRO GLN PRO LYS THR PHE GLY GLU SEQRES 2 A 470 LEU LYS ASN LEU PRO LEU LEU ASN THR ASP LYS PRO VAL SEQRES 3 A 470 GLN ALA LEU MET LYS ILE ALA ASP GLU LEU GLY GLU ILE SEQRES 4 A 470 PHE LYS PHE GLU ALA PRO GLY ARG VAL THR ARG TYR LEU SEQRES 5 A 470 SER SER GLN ARG LEU ILE LYS GLU ALA CYS ASP GLU SER SEQRES 6 A 470 ARG PHE ASP LYS ASN LEU SER GLN ALA LEU LYS PHE VAL SEQRES 7 A 470 ARG ASP PHE ALA GLY ASP GLY LEU PHE THR SER TRP THR SEQRES 8 A 470 HIS GLU LYS ASN TRP LYS LYS ALA HIS ASN ILE LEU LEU SEQRES 9 A 470 PRO SER PHE SER GLN GLN ALA MET LYS GLY TYR HIS ALA SEQRES 10 A 470 MET MET VAL ASP ILE ALA VAL GLN LEU VAL GLN LYS TRP SEQRES 11 A 470 GLU ARG LEU ASN ALA ASP GLU HIS ILE GLU VAL PRO GLU SEQRES 12 A 470 ASP MET THR ARG LEU THR LEU ASP THR ILE GLY LEU CYS SEQRES 13 A 470 GLY PHE ASN TYR ARG PHE ASN SER PHE TYR ARG ASP GLN SEQRES 14 A 470 PRO HIS PRO PHE ILE THR SER MET VAL ARG ALA LEU ASP SEQRES 15 A 470 GLU ALA MET ASN LYS LEU GLN ARG ALA ASN PRO ASP ASP SEQRES 16 A 470 PRO ALA TYR ASP GLU ASN LYS ARG GLN PHE GLN GLU ASP SEQRES 17 A 470 ILE LYS VAL MET ASN ASP LEU VAL ASP LYS ILE ILE ALA SEQRES 18 A 470 ASP ARG LYS ALA SER GLY GLU GLN SER ASP ASP LEU LEU SEQRES 19 A 470 THR HIS MET LEU ASN GLY LYS ASP PRO GLU THR GLY GLU SEQRES 20 A 470 PRO LEU ASP ASP GLU ASN ILE ARG TYR GLN ILE ILE THR SEQRES 21 A 470 PHE LEU ILE MET GLY HIS GLU THR THR SER GLY LEU LEU SEQRES 22 A 470 SER PHE ALA LEU TYR PHE LEU VAL LYS ASN PRO HIS VAL SEQRES 23 A 470 LEU GLN LYS ALA ALA GLU GLU ALA ALA ARG VAL LEU VAL SEQRES 24 A 470 ASP PRO VAL PRO SER TYR LYS GLN VAL LYS GLN LEU LYS SEQRES 25 A 470 TYR VAL GLY MET VAL LEU ASN GLU ALA LEU ARG LEU TRP SEQRES 26 A 470 PRO THR ALA PRO ALA PHE SER LEU TYR ALA LYS GLU ASP SEQRES 27 A 470 THR VAL LEU GLY GLY GLU TYR PRO LEU GLU LYS GLY ASP SEQRES 28 A 470 GLU LEU MET VAL LEU ILE PRO GLN LEU HIS ARG ASP LYS SEQRES 29 A 470 THR ILE TRP GLY ASP ASP VAL GLU GLU PHE ARG PRO GLU SEQRES 30 A 470 ARG PHE GLU ASN PRO SER ALA ILE PRO GLN HIS ALA PHE SEQRES 31 A 470 LYS PRO PHE GLY ASN GLY GLN ARG ALA CYS ILE GLY GLN SEQRES 32 A 470 GLN PHE ALA LEU HIS GLU ALA THR LEU VAL LEU GLY MET SEQRES 33 A 470 MET LEU LYS HIS PHE ASP PHE GLU ASP HIS THR ASN TYR SEQRES 34 A 470 GLU LEU ASP ILE LYS GLU THR LEU THR LEU LYS PRO GLU SEQRES 35 A 470 GLY PHE VAL VAL LYS ALA LYS SER LYS LYS ILE PRO LEU SEQRES 36 A 470 GLY GLY ILE PRO SER PRO SER THR GLU GLN SER ALA LYS SEQRES 37 A 470 LYS VAL SEQRES 1 B 470 THR ILE LYS GLU MET PRO GLN PRO LYS THR PHE GLY GLU SEQRES 2 B 470 LEU LYS ASN LEU PRO LEU LEU ASN THR ASP LYS PRO VAL SEQRES 3 B 470 GLN ALA LEU MET LYS ILE ALA ASP GLU LEU GLY GLU ILE SEQRES 4 B 470 PHE LYS PHE GLU ALA PRO GLY ARG VAL THR ARG TYR LEU SEQRES 5 B 470 SER SER GLN ARG LEU ILE LYS GLU ALA CYS ASP GLU SER SEQRES 6 B 470 ARG PHE ASP LYS ASN LEU SER GLN ALA LEU LYS PHE VAL SEQRES 7 B 470 ARG ASP PHE ALA GLY ASP GLY LEU PHE THR SER TRP THR SEQRES 8 B 470 HIS GLU LYS ASN TRP LYS LYS ALA HIS ASN ILE LEU LEU SEQRES 9 B 470 PRO SER PHE SER GLN GLN ALA MET LYS GLY TYR HIS ALA SEQRES 10 B 470 MET MET VAL ASP ILE ALA VAL GLN LEU VAL GLN LYS TRP SEQRES 11 B 470 GLU ARG LEU ASN ALA ASP GLU HIS ILE GLU VAL PRO GLU SEQRES 12 B 470 ASP MET THR ARG LEU THR LEU ASP THR ILE GLY LEU CYS SEQRES 13 B 470 GLY PHE ASN TYR ARG PHE ASN SER PHE TYR ARG ASP GLN SEQRES 14 B 470 PRO HIS PRO PHE ILE THR SER MET VAL ARG ALA LEU ASP SEQRES 15 B 470 GLU ALA MET ASN LYS LEU GLN ARG ALA ASN PRO ASP ASP SEQRES 16 B 470 PRO ALA TYR ASP GLU ASN LYS ARG GLN PHE GLN GLU ASP SEQRES 17 B 470 ILE LYS VAL MET ASN ASP LEU VAL ASP LYS ILE ILE ALA SEQRES 18 B 470 ASP ARG LYS ALA SER GLY GLU GLN SER ASP ASP LEU LEU SEQRES 19 B 470 THR HIS MET LEU ASN GLY LYS ASP PRO GLU THR GLY GLU SEQRES 20 B 470 PRO LEU ASP ASP GLU ASN ILE ARG TYR GLN ILE ILE THR SEQRES 21 B 470 PHE LEU ILE MET GLY HIS GLU THR THR SER GLY LEU LEU SEQRES 22 B 470 SER PHE ALA LEU TYR PHE LEU VAL LYS ASN PRO HIS VAL SEQRES 23 B 470 LEU GLN LYS ALA ALA GLU GLU ALA ALA ARG VAL LEU VAL SEQRES 24 B 470 ASP PRO VAL PRO SER TYR LYS GLN VAL LYS GLN LEU LYS SEQRES 25 B 470 TYR VAL GLY MET VAL LEU ASN GLU ALA LEU ARG LEU TRP SEQRES 26 B 470 PRO THR ALA PRO ALA PHE SER LEU TYR ALA LYS GLU ASP SEQRES 27 B 470 THR VAL LEU GLY GLY GLU TYR PRO LEU GLU LYS GLY ASP SEQRES 28 B 470 GLU LEU MET VAL LEU ILE PRO GLN LEU HIS ARG ASP LYS SEQRES 29 B 470 THR ILE TRP GLY ASP ASP VAL GLU GLU PHE ARG PRO GLU SEQRES 30 B 470 ARG PHE GLU ASN PRO SER ALA ILE PRO GLN HIS ALA PHE SEQRES 31 B 470 LYS PRO PHE GLY ASN GLY GLN ARG ALA CYS ILE GLY GLN SEQRES 32 B 470 GLN PHE ALA LEU HIS GLU ALA THR LEU VAL LEU GLY MET SEQRES 33 B 470 MET LEU LYS HIS PHE ASP PHE GLU ASP HIS THR ASN TYR SEQRES 34 B 470 GLU LEU ASP ILE LYS GLU THR LEU THR LEU LYS PRO GLU SEQRES 35 B 470 GLY PHE VAL VAL LYS ALA LYS SER LYS LYS ILE PRO LEU SEQRES 36 B 470 GLY GLY ILE PRO SER PRO SER THR GLU GLN SER ALA LYS SEQRES 37 B 470 LYS VAL HET PAM A 471 18 HET HEM A 472 43 HET HEM B 471 43 HETNAM PAM PALMITOLEIC ACID HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 PAM C16 H30 O2 FORMUL 4 HEM 2(C34 H32 FE N4 O4) FORMUL 6 HOH *172(H2 O) HELIX 1 1 PHE A 11 LYS A 15 5 5 HELIX 2 2 ASN A 16 LEU A 20 5 5 HELIX 3 3 LYS A 24 GLY A 37 1 14 HELIX 4 4 SER A 54 CYS A 62 1 9 HELIX 5 5 SER A 72 GLY A 83 1 12 HELIX 6 6 GLU A 93 LEU A 104 1 12 HELIX 7 7 PRO A 105 PHE A 107 5 3 HELIX 8 8 SER A 108 ARG A 132 1 25 HELIX 9 9 VAL A 141 ASN A 159 1 19 HELIX 10 10 ASN A 163 ARG A 167 5 5 HELIX 11 11 HIS A 171 LEU A 188 1 18 HELIX 12 12 ASP A 195 ALA A 197 5 3 HELIX 13 13 TYR A 198 SER A 226 1 29 HELIX 14 14 ASP A 232 GLY A 240 1 9 HELIX 15 15 ASP A 250 GLY A 265 1 16 HELIX 16 16 HIS A 266 LYS A 282 1 17 HELIX 17 17 ASN A 283 LEU A 298 1 16 HELIX 18 18 SER A 304 GLN A 310 1 7 HELIX 19 19 LEU A 311 TRP A 325 1 15 HELIX 20 20 ILE A 357 HIS A 361 1 5 HELIX 21 21 ASP A 363 GLY A 368 1 6 HELIX 22 22 ARG A 375 GLU A 380 5 6 HELIX 23 23 ASN A 395 ALA A 399 5 5 HELIX 24 24 GLY A 402 HIS A 420 1 19 HELIX 25 25 ASN B 16 ASN B 21 5 6 HELIX 26 26 LYS B 24 GLY B 37 1 14 HELIX 27 27 SER B 54 CYS B 62 1 9 HELIX 28 28 SER B 72 GLY B 83 1 12 HELIX 29 29 GLU B 93 LEU B 104 1 12 HELIX 30 30 PRO B 105 PHE B 107 5 3 HELIX 31 31 SER B 108 ARG B 132 1 25 HELIX 32 32 VAL B 141 ASN B 159 1 19 HELIX 33 33 ASN B 163 ARG B 167 5 5 HELIX 34 34 HIS B 171 LEU B 188 1 18 HELIX 35 35 ASP B 195 ASP B 199 5 5 HELIX 36 36 GLU B 200 LYS B 224 1 25 HELIX 37 37 ASP B 232 GLY B 240 1 9 HELIX 38 38 ASP B 250 GLY B 265 1 16 HELIX 39 39 HIS B 266 ASN B 283 1 18 HELIX 40 40 ASN B 283 LEU B 298 1 16 HELIX 41 41 SER B 304 LYS B 309 1 6 HELIX 42 42 LEU B 311 TRP B 325 1 15 HELIX 43 43 ILE B 357 HIS B 361 1 5 HELIX 44 44 ASP B 363 GLY B 368 1 6 HELIX 45 45 ARG B 375 GLU B 380 5 6 HELIX 46 46 ASN B 381 ILE B 385 5 5 HELIX 47 47 ASN B 395 ALA B 399 5 5 HELIX 48 48 GLY B 402 HIS B 420 1 19 SHEET 1 A 5 ILE A 39 ALA A 44 0 SHEET 2 A 5 ARG A 47 LEU A 52 -1 O ARG A 47 N ALA A 44 SHEET 3 A 5 GLU A 352 LEU A 356 1 O MET A 354 N ARG A 50 SHEET 4 A 5 ALA A 330 ALA A 335 -1 N LEU A 333 O LEU A 353 SHEET 5 A 5 PHE A 67 LYS A 69 -1 N ASP A 68 O TYR A 334 SHEET 1 B 3 ILE A 139 GLU A 140 0 SHEET 2 B 3 VAL A 445 SER A 450 -1 O VAL A 446 N ILE A 139 SHEET 3 B 3 PHE A 421 GLU A 424 -1 N GLU A 424 O LYS A 447 SHEET 1 C 2 THR A 339 LEU A 341 0 SHEET 2 C 2 TYR A 345 LEU A 347 -1 O LEU A 347 N THR A 339 SHEET 1 D 2 ILE A 433 GLU A 435 0 SHEET 2 D 2 LEU A 439 PRO A 441 -1 O LYS A 440 N LYS A 434 SHEET 1 E 5 ILE B 39 ALA B 44 0 SHEET 2 E 5 ARG B 47 LEU B 52 -1 O ARG B 47 N ALA B 44 SHEET 3 E 5 GLU B 352 LEU B 356 1 O MET B 354 N ARG B 50 SHEET 4 E 5 ALA B 330 ALA B 335 -1 N PHE B 331 O VAL B 355 SHEET 5 E 5 PHE B 67 LYS B 69 -1 N ASP B 68 O TYR B 334 SHEET 1 F 3 ILE B 139 GLU B 140 0 SHEET 2 F 3 VAL B 445 SER B 450 -1 O VAL B 446 N ILE B 139 SHEET 3 F 3 PHE B 421 GLU B 424 -1 N ASP B 422 O LYS B 449 SHEET 1 G 2 THR B 339 LEU B 341 0 SHEET 2 G 2 TYR B 345 LEU B 347 -1 O TYR B 345 N LEU B 341 SHEET 1 H 2 ILE B 433 GLU B 435 0 SHEET 2 H 2 LEU B 439 PRO B 441 -1 O LYS B 440 N LYS B 434 LINK SG CYS A 400 FE HEM A 472 1555 1555 2.18 LINK SG CYS B 400 FE HEM B 471 1555 1555 2.49 SITE 1 AC1 3 TYR A 51 VAL A 78 PHE A 87 SITE 1 AC2 15 LYS A 69 LEU A 86 PHE A 87 TRP A 96 SITE 2 AC2 15 MET A 264 THR A 268 PHE A 331 PRO A 392 SITE 3 AC2 15 ARG A 398 CYS A 400 HOH A 482 HOH A 486 SITE 4 AC2 15 HOH A 491 HOH A 504 HOH A 513 SITE 1 AC3 17 LYS B 69 LEU B 86 PHE B 87 TRP B 96 SITE 2 AC3 17 MET B 264 THR B 268 PHE B 331 PRO B 392 SITE 3 AC3 17 PHE B 393 ARG B 398 CYS B 400 ILE B 401 SITE 4 AC3 17 HOH B 476 HOH B 478 HOH B 487 HOH B 494 SITE 5 AC3 17 HOH B 497 CRYST1 63.769 125.171 153.943 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 0.015682 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006496 0.00000