HEADER OXIDOREDUCTASE 12-APR-10 2XBK TITLE X-RAY STRUCTURE OF THE SUBSTRATE-BOUND CYTOCHROME P450 PIMD - A TITLE 2 POLYENE MACROLIDE ANTIBIOTIC PIMARICIN EPOXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIMD PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 5-397; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: RESIDUES UPSTREAM OF SER 5 INCLUDING 6XHIS TAG ARE COMPND 7 ENGINEERED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES NATALENSIS; SOURCE 3 ORGANISM_TAXID: 68242; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PQE-30 KEYWDS EPOXIDATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.M.KELLS,H.OUELLET,J.SANTOS-ABERTURAS,J.F.APARICIO,L.M.PODUST REVDAT 5 20-DEC-23 2XBK 1 REMARK REVDAT 4 08-MAY-19 2XBK 1 REMARK REVDAT 3 15-SEP-10 2XBK 1 JRNL REVDAT 2 08-SEP-10 2XBK 1 JRNL REVDAT 1 04-AUG-10 2XBK 0 JRNL AUTH P.M.KELLS,H.OUELLET,J.SANTOS-ABERTURAS,J.F.APARICIO, JRNL AUTH 2 L.M.PODUST JRNL TITL STRUCTURE OF CYTOCHROME P450 PIMD SUGGESTS EPOXIDATION OF JRNL TITL 2 THE POLYENE MACROLIDE PIMARICIN OCCURS VIA A JRNL TITL 3 HYDROPEROXOFERRIC INTERMEDIATE. JRNL REF CHEM.BIOL. V. 17 841 2010 JRNL REFN ISSN 1074-5521 JRNL PMID 20797613 JRNL DOI 10.1016/J.CHEMBIOL.2010.05.026 REMARK 2 REMARK 2 RESOLUTION. 1.95 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 36749 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) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1912 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2700 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3006 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 89 REMARK 3 SOLVENT ATOMS : 272 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.89000 REMARK 3 B22 (A**2) : -0.09000 REMARK 3 B33 (A**2) : -0.88000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.245 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.439 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3325 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4557 ; 1.985 ; 2.042 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 419 ; 5.267 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;29.616 ;22.649 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 530 ;14.959 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;20.808 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 503 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2622 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2045 ; 1.896 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3305 ; 2.975 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1280 ; 5.052 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1252 ; 7.359 ; 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): 3325 ; 2.777 ; 3.000 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 : 1.40 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. RESIDUES WITH THE SIDE CHAIN MISSING FROM THE REMARK 3 ELECTRON DENSITY WERE MODELED AS ALANINE REMARK 4 REMARK 4 2XBK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-APR-10. REMARK 100 THE DEPOSITION ID IS D_1290043612. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11587 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38650 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 17.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 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: PDB ENTRY 2X9P REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM MALONATE, PH 7.0; 20% PEG REMARK 280 3330, T=23 C, TEMPERATURE 296K 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 49.96000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.84500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.96000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 49.84500 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 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 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 -6 REMARK 465 ARG A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 GLY A 4 REMARK 465 SER A 5 REMARK 465 HIS A 6 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 7 CG OD1 OD2 REMARK 470 LYS A 17 NZ REMARK 470 ARG A 26 CD NE CZ NH1 NH2 REMARK 470 GLU A 92 CD OE1 OE2 REMARK 470 ARG A 95 NE CZ NH1 NH2 REMARK 470 LYS A 382 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 OE2 GLU A 100 NH2 ARG A 103 1.79 REMARK 500 OE1 GLU A 100 NH1 ARG A 103 1.86 REMARK 500 NH1 ARG A 380 OE1 GLU A 392 2.04 REMARK 500 O HOH A 2128 O HOH A 2140 2.12 REMARK 500 OH TYR A 76 O HOH A 2069 2.17 REMARK 500 O HOH A 2186 O HOH A 2235 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2043 O HOH A 2209 2655 2.17 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 VAL A 157 CB VAL A 157 CG1 -0.126 REMARK 500 GLU A 221 CG GLU A 221 CD 0.115 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 PRO A 71 C - N - CA ANGL. DEV. = -10.9 DEGREES REMARK 500 LEU A 261 CB - CG - CD1 ANGL. DEV. = -10.3 DEGREES REMARK 500 ARG A 269 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 269 NE - CZ - NH2 ANGL. DEV. = -7.9 DEGREES REMARK 500 ARG A 279 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 302 NE - CZ - NH1 ANGL. DEV. = 4.1 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 LEU A 145 -65.08 -133.98 REMARK 500 ASP A 180 63.87 -166.39 REMARK 500 ASP A 180 63.56 -166.44 REMARK 500 LEU A 236 -74.37 -95.89 REMARK 500 PRO A 286 150.13 -49.25 REMARK 500 PRO A 335 46.09 -84.26 REMARK 500 TRP A 344 66.26 -110.75 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 A2042 DISTANCE = 6.64 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 4,5-DEEPOXYPIMARICIN: NON-EPOXIDATED PRECURSOR OF THE REMARK 600 POLYENE ANTIBIOTIC PIMARICIN OR NATAMYCIN. FORMED FROM REMARK 600 XBK, THE POLYENE MACROCYCLE, AND XBL, MYCOSAMINE SUGAR REMARK 600 PROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND TO CYS REMARK 600 346 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 A1398 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 346 SG REMARK 620 2 HEM A1398 NA 98.1 REMARK 620 3 HEM A1398 NB 88.7 88.7 REMARK 620 4 HEM A1398 NC 89.1 172.7 90.3 REMARK 620 5 HEM A1398 ND 100.3 90.5 170.9 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 HEM A 1398 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XBK A 1399 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2X9P RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE SUBSTRATE-FREE CYTOCHROME P450 PIMD - A REMARK 900 POLYENE MACROLIDE ANTIBIOTIC PIMARICIN EPOXIDASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 6XHIS TAG ENGINEERED AT THE N-TERMINUS UPSTREAM OF SER 5 DBREF 2XBK A 5 397 UNP Q9EW92 Q9EW92_9ACTO 5 397 SEQADV 2XBK MET A -6 UNP Q9EW92 EXPRESSION TAG SEQADV 2XBK ARG A -5 UNP Q9EW92 EXPRESSION TAG SEQADV 2XBK GLY A -4 UNP Q9EW92 EXPRESSION TAG SEQADV 2XBK SER A -3 UNP Q9EW92 EXPRESSION TAG SEQADV 2XBK HIS A -2 UNP Q9EW92 EXPRESSION TAG SEQADV 2XBK HIS A -1 UNP Q9EW92 EXPRESSION TAG SEQADV 2XBK HIS A 0 UNP Q9EW92 EXPRESSION TAG SEQADV 2XBK HIS A 1 UNP Q9EW92 EXPRESSION TAG SEQADV 2XBK HIS A 2 UNP Q9EW92 EXPRESSION TAG SEQADV 2XBK HIS A 3 UNP Q9EW92 EXPRESSION TAG SEQADV 2XBK GLY A 4 UNP Q9EW92 EXPRESSION TAG SEQRES 1 A 404 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER HIS SEQRES 2 A 404 ASP LEU PRO CYS LEU ASN LEU GLU PRO PRO LYS MET LEU SEQRES 3 A 404 LYS LEU SER PRO LEU LEU ARG ALA LEU GLN ASP ARG GLY SEQRES 4 A 404 PRO ILE HIS ARG VAL ARG THR PRO ALA GLY ASP GLU ALA SEQRES 5 A 404 TRP LEU VAL THR ARG HIS ALA GLU LEU LYS GLN LEU LEU SEQRES 6 A 404 HIS ASP GLU ARG ILE GLY ARG THR HIS PRO ASP PRO PRO SEQRES 7 A 404 SER ALA ALA GLN TYR VAL ARG SER PRO PHE LEU ASP LEU SEQRES 8 A 404 LEU ILE SER ASP ALA ASP ALA GLU SER GLY ARG ARG GLN SEQRES 9 A 404 HIS ALA GLU THR ARG ARG LEU LEU THR PRO LEU PHE SER SEQRES 10 A 404 ALA ARG ARG VAL LEU GLU MET GLN PRO LYS VAL GLU GLU SEQRES 11 A 404 ALA ALA ASP THR LEU LEU ASP ALA PHE ILE ALA GLN GLY SEQRES 12 A 404 PRO PRO GLY ASP LEU HIS GLY GLU LEU THR VAL PRO PHE SEQRES 13 A 404 ALA LEU THR VAL LEU CYS GLU VAL ILE GLY VAL PRO PRO SEQRES 14 A 404 GLN ARG ARG ALA GLU LEU THR THR LEU LEU ALA GLY ILE SEQRES 15 A 404 ALA LYS LEU ASP ASP ARG GLU GLY ALA VAL ARG ALA GLN SEQRES 16 A 404 ASP ASP LEU PHE GLY TYR VAL ALA GLY LEU VAL GLU HIS SEQRES 17 A 404 LYS ARG ALA GLU PRO GLY PRO ASP ILE ILE SER ARG LEU SEQRES 18 A 404 ASN ASP GLY GLU LEU THR GLU ASP ARG VAL ALA HIS LEU SEQRES 19 A 404 ALA MET GLY LEU LEU PHE ALA GLY LEU ASP SER VAL ALA SEQRES 20 A 404 SER ILE MET ASP ASN GLY VAL VAL LEU LEU ALA ALA HIS SEQRES 21 A 404 PRO ASP GLN ARG ALA ALA ALA LEU ALA ASP PRO ASP VAL SEQRES 22 A 404 MET ALA ARG ALA VAL GLU GLU VAL LEU ARG THR ALA ARG SEQRES 23 A 404 ALA GLY GLY SER VAL LEU PRO PRO ARG TYR ALA SER GLU SEQRES 24 A 404 ASP MET GLU PHE GLY GLY VAL THR ILE ARG ALA GLY ASP SEQRES 25 A 404 LEU VAL LEU PHE ASP LEU GLY LEU PRO ASN PHE ASP GLU SEQRES 26 A 404 ARG ALA PHE THR GLY PRO GLU GLU PHE ASP ALA ALA ARG SEQRES 27 A 404 THR PRO ASN PRO HIS LEU THR PHE GLY HIS GLY ILE TRP SEQRES 28 A 404 HIS CYS ILE GLY ALA PRO LEU ALA ARG LEU GLU LEU ARG SEQRES 29 A 404 THR MET PHE THR LYS LEU PHE THR ARG LEU PRO GLU LEU SEQRES 30 A 404 ARG PRO GLU LEU PRO VAL GLU GLN LEU ARG LEU LYS GLU SEQRES 31 A 404 GLY GLN LEU SER GLY GLY PHE ALA GLU LEU ARG VAL VAL SEQRES 32 A 404 TRP HET HEM A1398 43 HET XBK A1399 46 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM XBK 4,5-DE-EPOXYPIMARICIN HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 XBK C33 H47 N O12 FORMUL 4 HOH *272(H2 O) HELIX 1 1 SER A 22 GLY A 32 1 11 HELIX 2 2 ARG A 50 LEU A 58 1 9 HELIX 3 3 ASP A 69 ALA A 73 5 5 HELIX 4 4 SER A 79 LEU A 84 1 6 HELIX 5 5 ASP A 90 THR A 106 1 17 HELIX 6 6 PRO A 107 PHE A 109 5 3 HELIX 7 7 SER A 110 GLN A 135 1 26 HELIX 8 8 LEU A 141 GLY A 159 1 19 HELIX 9 9 PRO A 161 GLN A 163 5 3 HELIX 10 10 ARG A 164 ALA A 176 1 13 HELIX 11 11 ASP A 180 GLU A 205 1 26 HELIX 12 12 ASP A 209 ASP A 216 1 8 HELIX 13 13 THR A 220 GLY A 235 1 16 HELIX 14 14 LEU A 236 HIS A 253 1 18 HELIX 15 15 HIS A 253 ASP A 263 1 11 HELIX 16 16 ASP A 263 ALA A 278 1 16 HELIX 17 17 LEU A 311 PHE A 316 1 6 HELIX 18 18 GLY A 348 LEU A 367 1 20 HELIX 19 19 PRO A 375 LEU A 379 5 5 SHEET 1 AA 5 ILE A 34 ARG A 38 0 SHEET 2 AA 5 GLU A 44 VAL A 48 -1 O ALA A 45 N VAL A 37 SHEET 3 AA 5 LEU A 306 LEU A 308 1 O LEU A 306 N TRP A 46 SHEET 4 AA 5 ARG A 288 ALA A 290 -1 O ARG A 288 N VAL A 307 SHEET 5 AA 5 ILE A 63 GLY A 64 -1 O GLY A 64 N TYR A 289 SHEET 1 AB 3 GLY A 139 ASP A 140 0 SHEET 2 AB 3 ARG A 394 VAL A 396 -1 O VAL A 395 N GLY A 139 SHEET 3 AB 3 ARG A 371 PRO A 372 -1 O ARG A 371 N VAL A 396 SHEET 1 AC 2 MET A 294 PHE A 296 0 SHEET 2 AC 2 VAL A 299 ILE A 301 -1 O VAL A 299 N PHE A 296 SHEET 1 AD 2 GLY A 340 HIS A 341 0 SHEET 2 AD 2 TRP A 344 HIS A 345 -1 O TRP A 344 N HIS A 341 LINK SG CYS A 346 FE HEM A1398 1555 1555 2.38 CISPEP 1 PRO A 137 PRO A 138 0 -8.78 CISPEP 2 THR A 332 PRO A 333 0 -2.37 SITE 1 AC1 27 ARG A 65 HIS A 98 ARG A 102 PHE A 109 SITE 2 AC1 27 LEU A 154 LEU A 231 ALA A 234 GLY A 235 SITE 3 AC1 27 SER A 238 VAL A 239 ILE A 242 PRO A 286 SITE 4 AC1 27 ARG A 288 LEU A 311 THR A 338 PHE A 339 SITE 5 AC1 27 GLY A 340 ILE A 343 TRP A 344 CYS A 346 SITE 6 AC1 27 ILE A 347 GLY A 348 ALA A 352 XBK A1399 SITE 7 AC1 27 HOH A2168 HOH A2268 HOH A2269 SITE 1 AC2 17 ARG A 65 LEU A 178 PHE A 233 SER A 238 SITE 2 AC2 17 SER A 241 ARG A 279 SER A 283 VAL A 284 SITE 3 AC2 17 SER A 387 GLY A 388 GLY A 389 HEM A1398 SITE 4 AC2 17 HOH A2168 HOH A2261 HOH A2270 HOH A2271 SITE 5 AC2 17 HOH A2272 CRYST1 99.920 99.690 58.505 90.00 111.92 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 0.010008 0.000000 0.004027 0.00000 SCALE2 0.000000 0.010031 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018425 0.00000