PDB Short entry for 1SMI HEADER OXIDOREDUCTASE 09-MAR-04 1SMI TITLE A SINGLE MUTATION OF P450 BM3 INDUCES THE CONFORMATIONAL REARRANGEMENT TITLE 2 SEEN UPON SUBSTRATE-BINDING IN WILD-TYPE ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL P-450:NADPH-P450 REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CYTOCHROME P450 102; COMPND 5 SYNONYM: CYTOCHROME P450(BM-3); P450BM-3 [INCLUDES: CYTOCHROME P450 COMPND 6 102, NADPH--CYTOCHROME P450 REDUCTASE]; ;CYTOCHROME P-450:NADPH-P-450 COMPND 7 REDUCTASE; COMPND 8 EC: 1.14.14.1; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS MEGATERIUM; SOURCE 3 ORGANISM_TAXID: 1404; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS MONOOXYGENASE; FATTY ACID OXYGENASE; CYTOCHROME P450; SUBSTRATE KEYWDS 2 BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.G.JOYCE,H.M.GIRVAN,A.W.MUNRO,D.LEYS REVDAT 4 23-AUG-23 1SMI 1 REMARK REVDAT 3 27-OCT-21 1SMI 1 REMARK SEQADV REVDAT 2 24-FEB-09 1SMI 1 VERSN REVDAT 1 08-JUN-04 1SMI 0 JRNL AUTH M.G.JOYCE,H.M.GIRVAN,A.W.MUNRO,D.LEYS JRNL TITL A SINGLE MUTATION IN CYTOCHROME P450 BM3 INDUCES THE JRNL TITL 2 CONFORMATIONAL REARRANGEMENT SEEN UPON SUBSTRATE BINDING IN JRNL TITL 3 THE WILD-TYPE ENZYME JRNL REF J.BIOL.CHEM. V. 279 23287 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15020590 JRNL DOI 10.1074/JBC.M401717200 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.9999 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 65010 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3440 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4818 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 274 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7124 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 492 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 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): 0.216 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.202 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.222 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7387 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10021 ; 1.719 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 888 ; 6.906 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 354 ;36.330 ;24.718 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1275 ;17.131 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;16.963 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1072 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5649 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3870 ; 0.239 ; 0.200 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): 605 ; 0.187 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.013 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 61 ; 0.172 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.151 ; 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): 4621 ; 1.125 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7177 ; 1.683 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3177 ; 2.568 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2841 ; 3.719 ; 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 : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 1SMI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000021829. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 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) : 0.900 REMARK 200 MONOCHROMATOR : SYNCHROTRON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68550 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.410 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1JPZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000, MME, 10MM MANGANESE REMARK 280 SULPHATE, PH 6.3, 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 30.60300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.16900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.46450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.16900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.60300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.46450 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 SER A 108 REMARK 465 PRO A 193 REMARK 465 ASP A 194 REMARK 465 ASP A 195 REMARK 465 PRO A 196 REMARK 465 ALA A 197 REMARK 465 TYR A 198 REMARK 465 ASP A 199 REMARK 465 GLU A 200 REMARK 465 ASN A 201 REMARK 465 LYS A 202 REMARK 465 ARG A 203 REMARK 465 SER A 226 REMARK 465 GLY A 227 REMARK 465 GLU A 228 REMARK 465 GLN A 229 REMARK 465 SER A 230 REMARK 465 GLY A 457 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 ARG A 471 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 465 ARG B 471 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 15 CB CG CD CE NZ REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 GLN A 109 CG CD OE1 NE2 REMARK 470 GLN A 110 CB CG CD OE1 NE2 REMARK 470 ASP A 136 CG OD1 OD2 REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 ASN A 192 CB CG OD1 ND2 REMARK 470 LYS A 218 CG CD CE NZ REMARK 470 ALA A 384 CB REMARK 470 ILE B 2 CG1 CG2 CD1 REMARK 470 LYS B 3 CG CD CE NZ REMARK 470 GLU B 4 CG CD OE1 OE2 REMARK 470 LYS B 9 CG CD CE NZ REMARK 470 LEU B 14 CG CD1 CD2 REMARK 470 LYS B 15 CB CG CD CE NZ REMARK 470 LEU B 20 CG CD1 CD2 REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 VAL B 178 CB CG1 CG2 REMARK 470 GLN B 229 CG CD OE1 NE2 REMARK 470 LYS B 241 CB CG CD CE NZ REMARK 470 LYS B 306 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 A 547 O HOH A 593 1.91 REMARK 500 O HOH A 567 O HOH A 758 2.03 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 ASP A 80 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 144 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 369 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP B 250 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 370 CB - CG - OD2 ANGL. DEV. = 6.3 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 -132.24 59.18 REMARK 500 LEU A 20 55.21 -119.39 REMARK 500 GLN A 110 -47.39 140.70 REMARK 500 GLU A 244 -79.10 -142.89 REMARK 500 ILE A 263 -68.49 -93.57 REMARK 500 HIS A 266 -30.25 -142.92 REMARK 500 LYS A 349 128.78 -37.75 REMARK 500 SER A 383 29.41 -64.69 REMARK 500 ALA A 384 24.15 -154.53 REMARK 500 LEU A 437 54.79 30.14 REMARK 500 GLU B 4 88.63 -61.41 REMARK 500 LYS B 9 141.05 68.08 REMARK 500 GLU B 13 -36.55 -131.78 REMARK 500 LYS B 15 -105.90 65.19 REMARK 500 PRO B 45 105.72 -56.67 REMARK 500 ASP B 84 35.93 -90.71 REMARK 500 ASP B 136 0.23 -57.27 REMARK 500 SER B 176 -70.92 -51.27 REMARK 500 ASP B 195 122.27 -26.60 REMARK 500 LYS B 224 -15.34 -48.32 REMARK 500 ASP B 231 59.04 -115.56 REMARK 500 ASP B 250 155.27 -32.59 REMARK 500 ILE B 263 -83.82 -71.28 REMARK 500 HIS B 266 -32.93 -140.72 REMARK 500 ASP B 370 33.38 -91.22 REMARK 500 ARG B 378 -27.84 -39.98 REMARK 500 LYS B 391 47.40 -143.51 REMARK 500 ASN B 428 75.30 37.05 REMARK 500 THR B 436 51.58 -145.15 REMARK 500 LEU B 437 -14.26 68.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 437 THR A 438 136.21 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 GLU A 264 OE1 REMARK 620 2 HEM A 472 NA 83.3 REMARK 620 3 HEM A 472 NB 85.2 93.7 REMARK 620 4 HEM A 472 NC 89.8 172.9 84.2 REMARK 620 5 HEM A 472 ND 85.8 84.3 170.9 96.7 REMARK 620 6 CYS A 400 SG 173.3 102.8 91.5 84.1 97.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 472 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 400 SG REMARK 620 2 HEM B 472 NA 99.7 REMARK 620 3 HEM B 472 NB 88.0 90.5 REMARK 620 4 HEM B 472 NC 87.1 173.1 88.5 REMARK 620 5 HEM B 472 ND 98.1 88.4 173.8 91.9 REMARK 620 6 HOH B 496 O 171.4 85.7 85.2 87.4 88.7 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 472 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 472 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FAG RELATED DB: PDB REMARK 900 WILD TYPE ENZYME WITH SUBSTRATE BOUND REMARK 900 RELATED ID: 1JPZ RELATED DB: PDB REMARK 900 WILD TYPE ENZYME WITH N-PALMITOYL GLYCINE BOUND REMARK 900 RELATED ID: 1BU7 RELATED DB: PDB REMARK 900 WILD TYPE ENZYME WITHOUT SUBSTRATE REMARK 900 RELATED ID: 1SMJ RELATED DB: PDB REMARK 900 THE A264E MUTANT WITH SUBSTRATE DBREF 1SMI A 1 471 UNP P14779 CPXB_BACME 1 471 DBREF 1SMI B 1 471 UNP P14779 CPXB_BACME 1 471 SEQADV 1SMI GLU A 264 UNP P14779 ALA 264 ENGINEERED MUTATION SEQADV 1SMI GLU B 264 UNP P14779 ALA 264 ENGINEERED MUTATION SEQRES 1 A 471 THR ILE LYS GLU MET PRO GLN PRO LYS THR PHE GLY GLU SEQRES 2 A 471 LEU LYS ASN LEU PRO LEU LEU ASN THR ASP LYS PRO VAL SEQRES 3 A 471 GLN ALA LEU MET LYS ILE ALA ASP GLU LEU GLY GLU ILE SEQRES 4 A 471 PHE LYS PHE GLU ALA PRO GLY ARG VAL THR ARG TYR LEU SEQRES 5 A 471 SER SER GLN ARG LEU ILE LYS GLU ALA CYS ASP GLU SER SEQRES 6 A 471 ARG PHE ASP LYS ASN LEU SER GLN ALA LEU LYS PHE VAL SEQRES 7 A 471 ARG ASP PHE ALA GLY ASP GLY LEU PHE THR SER TRP THR SEQRES 8 A 471 HIS GLU LYS ASN TRP LYS LYS ALA HIS ASN ILE LEU LEU SEQRES 9 A 471 PRO SER PHE SER GLN GLN ALA MET LYS GLY TYR HIS ALA SEQRES 10 A 471 MET MET VAL ASP ILE ALA VAL GLN LEU VAL GLN LYS TRP SEQRES 11 A 471 GLU ARG LEU ASN ALA ASP GLU HIS ILE GLU VAL PRO GLU SEQRES 12 A 471 ASP MET THR ARG LEU THR LEU ASP THR ILE GLY LEU CYS SEQRES 13 A 471 GLY PHE ASN TYR ARG PHE ASN SER PHE TYR ARG ASP GLN SEQRES 14 A 471 PRO HIS PRO PHE ILE THR SER MET VAL ARG ALA LEU ASP SEQRES 15 A 471 GLU ALA MET ASN LYS LEU GLN ARG ALA ASN PRO ASP ASP SEQRES 16 A 471 PRO ALA TYR ASP GLU ASN LYS ARG GLN PHE GLN GLU ASP SEQRES 17 A 471 ILE LYS VAL MET ASN ASP LEU VAL ASP LYS ILE ILE ALA SEQRES 18 A 471 ASP ARG LYS ALA SER GLY GLU GLN SER ASP ASP LEU LEU SEQRES 19 A 471 THR HIS MET LEU ASN GLY LYS ASP PRO GLU THR GLY GLU SEQRES 20 A 471 PRO LEU ASP ASP GLU ASN ILE ARG TYR GLN ILE ILE THR SEQRES 21 A 471 PHE LEU ILE GLU GLY HIS GLU THR THR SER GLY LEU LEU SEQRES 22 A 471 SER PHE ALA LEU TYR PHE LEU VAL LYS ASN PRO HIS VAL SEQRES 23 A 471 LEU GLN LYS ALA ALA GLU GLU ALA ALA ARG VAL LEU VAL SEQRES 24 A 471 ASP PRO VAL PRO SER TYR LYS GLN VAL LYS GLN LEU LYS SEQRES 25 A 471 TYR VAL GLY MET VAL LEU ASN GLU ALA LEU ARG LEU TRP SEQRES 26 A 471 PRO THR ALA PRO ALA PHE SER LEU TYR ALA LYS GLU ASP SEQRES 27 A 471 THR VAL LEU GLY GLY GLU TYR PRO LEU GLU LYS GLY ASP SEQRES 28 A 471 GLU LEU MET VAL LEU ILE PRO GLN LEU HIS ARG ASP LYS SEQRES 29 A 471 THR ILE TRP GLY ASP ASP VAL GLU GLU PHE ARG PRO GLU SEQRES 30 A 471 ARG PHE GLU ASN PRO SER ALA ILE PRO GLN HIS ALA PHE SEQRES 31 A 471 LYS PRO PHE GLY ASN GLY GLN ARG ALA CYS ILE GLY GLN SEQRES 32 A 471 GLN PHE ALA LEU HIS GLU ALA THR LEU VAL LEU GLY MET SEQRES 33 A 471 MET LEU LYS HIS PHE ASP PHE GLU ASP HIS THR ASN TYR SEQRES 34 A 471 GLU LEU ASP ILE LYS GLU THR LEU THR LEU LYS PRO GLU SEQRES 35 A 471 GLY PHE VAL VAL LYS ALA LYS SER LYS LYS ILE PRO LEU SEQRES 36 A 471 GLY GLY ILE PRO SER PRO SER THR GLU GLN SER ALA LYS SEQRES 37 A 471 LYS VAL ARG SEQRES 1 B 471 THR ILE LYS GLU MET PRO GLN PRO LYS THR PHE GLY GLU SEQRES 2 B 471 LEU LYS ASN LEU PRO LEU LEU ASN THR ASP LYS PRO VAL SEQRES 3 B 471 GLN ALA LEU MET LYS ILE ALA ASP GLU LEU GLY GLU ILE SEQRES 4 B 471 PHE LYS PHE GLU ALA PRO GLY ARG VAL THR ARG TYR LEU SEQRES 5 B 471 SER SER GLN ARG LEU ILE LYS GLU ALA CYS ASP GLU SER SEQRES 6 B 471 ARG PHE ASP LYS ASN LEU SER GLN ALA LEU LYS PHE VAL SEQRES 7 B 471 ARG ASP PHE ALA GLY ASP GLY LEU PHE THR SER TRP THR SEQRES 8 B 471 HIS GLU LYS ASN TRP LYS LYS ALA HIS ASN ILE LEU LEU SEQRES 9 B 471 PRO SER PHE SER GLN GLN ALA MET LYS GLY TYR HIS ALA SEQRES 10 B 471 MET MET VAL ASP ILE ALA VAL GLN LEU VAL GLN LYS TRP SEQRES 11 B 471 GLU ARG LEU ASN ALA ASP GLU HIS ILE GLU VAL PRO GLU SEQRES 12 B 471 ASP MET THR ARG LEU THR LEU ASP THR ILE GLY LEU CYS SEQRES 13 B 471 GLY PHE ASN TYR ARG PHE ASN SER PHE TYR ARG ASP GLN SEQRES 14 B 471 PRO HIS PRO PHE ILE THR SER MET VAL ARG ALA LEU ASP SEQRES 15 B 471 GLU ALA MET ASN LYS LEU GLN ARG ALA ASN PRO ASP ASP SEQRES 16 B 471 PRO ALA TYR ASP GLU ASN LYS ARG GLN PHE GLN GLU ASP SEQRES 17 B 471 ILE LYS VAL MET ASN ASP LEU VAL ASP LYS ILE ILE ALA SEQRES 18 B 471 ASP ARG LYS ALA SER GLY GLU GLN SER ASP ASP LEU LEU SEQRES 19 B 471 THR HIS MET LEU ASN GLY LYS ASP PRO GLU THR GLY GLU SEQRES 20 B 471 PRO LEU ASP ASP GLU ASN ILE ARG TYR GLN ILE ILE THR SEQRES 21 B 471 PHE LEU ILE GLU GLY HIS GLU THR THR SER GLY LEU LEU SEQRES 22 B 471 SER PHE ALA LEU TYR PHE LEU VAL LYS ASN PRO HIS VAL SEQRES 23 B 471 LEU GLN LYS ALA ALA GLU GLU ALA ALA ARG VAL LEU VAL SEQRES 24 B 471 ASP PRO VAL PRO SER TYR LYS GLN VAL LYS GLN LEU LYS SEQRES 25 B 471 TYR VAL GLY MET VAL LEU ASN GLU ALA LEU ARG LEU TRP SEQRES 26 B 471 PRO THR ALA PRO ALA PHE SER LEU TYR ALA LYS GLU ASP SEQRES 27 B 471 THR VAL LEU GLY GLY GLU TYR PRO LEU GLU LYS GLY ASP SEQRES 28 B 471 GLU LEU MET VAL LEU ILE PRO GLN LEU HIS ARG ASP LYS SEQRES 29 B 471 THR ILE TRP GLY ASP ASP VAL GLU GLU PHE ARG PRO GLU SEQRES 30 B 471 ARG PHE GLU ASN PRO SER ALA ILE PRO GLN HIS ALA PHE SEQRES 31 B 471 LYS PRO PHE GLY ASN GLY GLN ARG ALA CYS ILE GLY GLN SEQRES 32 B 471 GLN PHE ALA LEU HIS GLU ALA THR LEU VAL LEU GLY MET SEQRES 33 B 471 MET LEU LYS HIS PHE ASP PHE GLU ASP HIS THR ASN TYR SEQRES 34 B 471 GLU LEU ASP ILE LYS GLU THR LEU THR LEU LYS PRO GLU SEQRES 35 B 471 GLY PHE VAL VAL LYS ALA LYS SER LYS LYS ILE PRO LEU SEQRES 36 B 471 GLY GLY ILE PRO SER PRO SER THR GLU GLN SER ALA LYS SEQRES 37 B 471 LYS VAL ARG HET HEM A 472 43 HET HEM B 472 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *492(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 GLN A 110 ARG A 132 1 23 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 LYS A 187 1 17 HELIX 12 12 LEU A 188 ARG A 190 5 3 HELIX 13 13 GLN A 204 ALA A 225 1 22 HELIX 14 14 ASP A 232 GLY A 240 1 9 HELIX 15 15 ASP A 250 GLU A 264 1 15 HELIX 16 16 HIS A 266 ASN A 283 1 18 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 ALA B 197 5 3 HELIX 36 36 TYR B 198 SER B 226 1 29 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 GLN B 310 1 7 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 THR A 49 N PHE A 42 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 PHE A 331 O VAL A 355 SHEET 5 A 5 PHE A 67 ASN A 70 -1 N ASN A 70 O SER A 332 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 ASP A 422 O LYS A 449 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 LEU B 52 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 LEU B 347 N THR B 339 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 OE1 GLU A 264 FE HEM A 472 1555 1555 1.95 LINK SG CYS A 400 FE HEM A 472 1555 1555 2.30 LINK SG CYS B 400 FE HEM B 472 1555 1555 2.46 LINK FE HEM B 472 O HOH B 496 1555 1555 2.56 SITE 1 AC1 27 LYS A 69 LEU A 86 PHE A 87 TRP A 96 SITE 2 AC1 27 PHE A 261 GLU A 264 GLY A 265 THR A 268 SITE 3 AC1 27 THR A 269 LEU A 272 THR A 327 PHE A 331 SITE 4 AC1 27 PRO A 392 PHE A 393 GLY A 394 ARG A 398 SITE 5 AC1 27 ALA A 399 CYS A 400 ILE A 401 GLY A 402 SITE 6 AC1 27 ALA A 406 HOH A 475 HOH A 476 HOH A 489 SITE 7 AC1 27 HOH A 492 HOH A 535 HOH A 538 SITE 1 AC2 26 LYS B 69 LEU B 86 PHE B 87 TRP B 96 SITE 2 AC2 26 PHE B 261 GLU B 264 GLY B 265 THR B 268 SITE 3 AC2 26 THR B 269 THR B 327 PHE B 331 PRO B 392 SITE 4 AC2 26 PHE B 393 GLY B 394 ARG B 398 ALA B 399 SITE 5 AC2 26 CYS B 400 ILE B 401 GLY B 402 ALA B 406 SITE 6 AC2 26 HOH B 482 HOH B 483 HOH B 491 HOH B 496 SITE 7 AC2 26 HOH B 511 HOH B 559 CRYST1 61.206 118.929 146.338 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 0.016338 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008408 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006833 0.00000