HEADER OXIDOREDUCTASE/ANTIBIOTIC 04-DEC-09 3ABA TITLE CRYSTAL STRUCTURE OF CYP105P1 IN COMPLEX WITH FILIPIN I COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME P450 HYDROXYLASE, CYP105P1; COMPND 5 EC: 1.14.13.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AVERMITILIS; SOURCE 3 ORGANISM_TAXID: 33903; SOURCE 4 STRAIN: MA-4680; SOURCE 5 GENE: PTEC, SAV413, SAV_413; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 CODONPLUS (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS P450, OXIDOREDUCTASE, HEME, MONOOXYGENASE, MACROLIDE, FILIPIN, IRON, KEYWDS 2 METAL-BINDING, OXIDOREDUCTASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.H.XU,S.FUSHINOBU,S.TAKAMATSU,T.WAKAGI,H.IKEDA,H.SHOUN REVDAT 4 01-NOV-23 3ABA 1 REMARK SEQADV REVDAT 3 13-JUL-11 3ABA 1 VERSN REVDAT 2 01-SEP-10 3ABA 1 JRNL REVDAT 1 07-APR-10 3ABA 0 JRNL AUTH L.H.XU,S.FUSHINOBU,S.TAKAMATSU,T.WAKAGI,H.IKEDA,H.SHOUN JRNL TITL REGIO- AND STEREOSPECIFICITY OF FILIPIN HYDROXYLATION SITES JRNL TITL 2 REVEALED BY CRYSTAL STRUCTURES OF CYTOCHROME P450 105P1 AND JRNL TITL 3 105D6 FROM STREPTOMYCES AVERMITILIS JRNL REF J.BIOL.CHEM. V. 285 16844 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20375018 JRNL DOI 10.1074/JBC.M109.092460 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.H.XU,S.FUSHINOBU,H.IKEDA,T.WAKAGI,H.SHOUN REMARK 1 TITL CRYSTAL STRUCTURES OF CYTOCHROME P450 105P1 FROM REMARK 1 TITL 2 STREPTOMYCES AVERMITILIS: CONFORMATIONAL FLEXIBILITY AND REMARK 1 TITL 3 HISTIDINE LIGATION STATE REMARK 1 REF J.BACTERIOL. V. 191 1211 2009 REMARK 1 REFN ISSN 0021-9193 REMARK 1 PMID 19074393 REMARK 1 DOI 10.1128/JB.01276-08 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 55867 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2980 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4122 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE SET COUNT : 225 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3081 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 592 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 25.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.03000 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): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.688 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3253 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4434 ; 2.138 ; 2.020 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 396 ; 5.732 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;32.705 ;23.113 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 508 ;14.633 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;20.008 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 494 ; 0.177 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2495 ; 0.014 ; 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): 1979 ; 1.249 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3186 ; 2.035 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1274 ; 3.570 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1248 ; 5.307 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 82 REMARK 3 ORIGIN FOR THE GROUP (A): -7.7820 33.8000 26.4600 REMARK 3 T TENSOR REMARK 3 T11: 0.0508 T22: 0.1067 REMARK 3 T33: 0.0934 T12: -0.0400 REMARK 3 T13: 0.0624 T23: -0.0384 REMARK 3 L TENSOR REMARK 3 L11: 0.5062 L22: 0.5719 REMARK 3 L33: 1.0047 L12: -0.0257 REMARK 3 L13: -0.0399 L23: 0.0402 REMARK 3 S TENSOR REMARK 3 S11: -0.0479 S12: -0.0330 S13: -0.0494 REMARK 3 S21: 0.1229 S22: -0.0543 S23: 0.1122 REMARK 3 S31: 0.0737 S32: -0.2006 S33: 0.1021 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 83 A 146 REMARK 3 ORIGIN FOR THE GROUP (A): 11.5400 45.1990 11.4190 REMARK 3 T TENSOR REMARK 3 T11: 0.0754 T22: 0.0832 REMARK 3 T33: 0.0722 T12: -0.0019 REMARK 3 T13: -0.0162 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 0.2256 L22: 0.5298 REMARK 3 L33: 0.2582 L12: -0.3272 REMARK 3 L13: -0.0581 L23: 0.0846 REMARK 3 S TENSOR REMARK 3 S11: -0.0176 S12: 0.0032 S13: 0.0118 REMARK 3 S21: -0.0334 S22: -0.0244 S23: 0.0081 REMARK 3 S31: -0.0239 S32: -0.0084 S33: 0.0419 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 147 A 323 REMARK 3 ORIGIN FOR THE GROUP (A): 6.0640 43.0370 17.8180 REMARK 3 T TENSOR REMARK 3 T11: 0.0728 T22: 0.0888 REMARK 3 T33: 0.0682 T12: -0.0087 REMARK 3 T13: 0.0094 T23: -0.0225 REMARK 3 L TENSOR REMARK 3 L11: 0.0812 L22: 0.2406 REMARK 3 L33: 0.3367 L12: -0.0119 REMARK 3 L13: -0.0533 L23: 0.0943 REMARK 3 S TENSOR REMARK 3 S11: -0.0265 S12: 0.0206 S13: 0.0001 REMARK 3 S21: 0.0348 S22: -0.0231 S23: 0.0449 REMARK 3 S31: -0.0088 S32: -0.0348 S33: 0.0495 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 324 A 403 REMARK 3 ORIGIN FOR THE GROUP (A): 10.4220 29.4200 11.8800 REMARK 3 T TENSOR REMARK 3 T11: 0.0866 T22: 0.0867 REMARK 3 T33: 0.0734 T12: -0.0105 REMARK 3 T13: 0.0130 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.4303 L22: 0.2617 REMARK 3 L33: 0.2756 L12: -0.1616 REMARK 3 L13: -0.2797 L23: 0.1939 REMARK 3 S TENSOR REMARK 3 S11: -0.0390 S12: 0.0306 S13: -0.0255 REMARK 3 S21: 0.0352 S22: -0.0498 S23: 0.0493 REMARK 3 S31: 0.0620 S32: -0.0205 S33: 0.0887 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 : 1.40 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 3ABA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000029042. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59975 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.90 REMARK 200 R MERGE FOR SHELL (I) : 0.46500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3E5J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (NH4)2SO4, LI2SO4, PH 10.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 75.61950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.68400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.68400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.80975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.68400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.68400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 113.42925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.68400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.68400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.80975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.68400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.68400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 113.42925 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.61950 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 536 LIES ON A SPECIAL POSITION. 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 PRO A 2 REMARK 465 GLU A 3 REMARK 465 PRO A 4 REMARK 465 THR A 5 REMARK 465 ALA A 6 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 725 O HOH A 926 2.12 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 GLU A 92 CG GLU A 92 CD 0.096 REMARK 500 ARG A 115 CZ ARG A 115 NH1 0.086 REMARK 500 PHE A 286 CE1 PHE A 286 CZ 0.128 REMARK 500 VAL A 388 CB VAL A 388 CG2 0.141 REMARK 500 GLU A 394 CD GLU A 394 OE1 0.093 REMARK 500 HIS A 403 C HIS A 403 O 0.134 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 101 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 109 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 153 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 161 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 MET A 172 CG - SD - CE ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG A 200 NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 355 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 355 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 HIS A 403 CA - C - O ANGL. DEV. = -16.3 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 ALA A 32 83.25 -160.72 REMARK 500 LEU A 87 -54.71 69.67 REMARK 500 PHE A 142 -58.24 -151.20 REMARK 500 ASN A 203 71.56 -152.89 REMARK 500 THR A 282 82.37 13.70 REMARK 500 LYS A 305 129.02 -39.99 REMARK 500 CYS A 348 116.57 -38.91 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 A1408 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 348 SG REMARK 620 2 HEM A1408 NA 105.0 REMARK 620 3 HEM A1408 NB 95.7 86.3 REMARK 620 4 HEM A1408 NC 87.2 167.7 91.6 REMARK 620 5 HEM A1408 ND 98.3 90.1 166.0 88.9 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 1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLI A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 407 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3E5J RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH NO LIGANDS REMARK 900 RELATED ID: 3E5K RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH 4-PHENYLIMIDAZOLE REMARK 900 RELATED ID: 3E5L RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH H72A MUTATION REMARK 900 RELATED ID: 3ABB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CYP105D6 DBREF 3ABA A 1 399 UNP Q93H81 Q93H81_STRAW 1 399 SEQADV 3ABA HIS A 400 UNP Q93H81 EXPRESSION TAG SEQADV 3ABA HIS A 401 UNP Q93H81 EXPRESSION TAG SEQADV 3ABA HIS A 402 UNP Q93H81 EXPRESSION TAG SEQADV 3ABA HIS A 403 UNP Q93H81 EXPRESSION TAG SEQRES 1 A 403 MET PRO GLU PRO THR ALA ASP ALA PRO THR VAL PRO LYS SEQRES 2 A 403 ALA ARG SER CYS PRO PHE LEU PRO PRO ASP GLY ILE ALA SEQRES 3 A 403 ASP ILE ARG ALA ALA ALA PRO VAL THR ARG ALA THR PHE SEQRES 4 A 403 THR SER GLY HIS GLU ALA TRP LEU VAL THR GLY TYR GLU SEQRES 5 A 403 GLU VAL ARG ALA LEU LEU ARG ASP SER SER PHE SER VAL SEQRES 6 A 403 GLN VAL PRO HIS ALA LEU HIS THR GLN ASP GLY VAL VAL SEQRES 7 A 403 THR GLN LYS PRO GLY ARG GLY SER LEU LEU TRP GLN ASP SEQRES 8 A 403 GLU PRO GLU HIS THR SER ASP ARG LYS LEU LEU ALA LYS SEQRES 9 A 403 GLU PHE THR VAL ARG ARG MET GLN ALA LEU ARG PRO ASN SEQRES 10 A 403 ILE GLN ARG ILE VAL ASP GLU HIS LEU ASP ALA ILE GLU SEQRES 11 A 403 ALA ARG GLY GLY PRO VAL ASP LEU VAL LYS THR PHE ALA SEQRES 12 A 403 ASN ALA VAL PRO SER MET VAL ILE SER ASP LEU PHE GLY SEQRES 13 A 403 VAL PRO VAL GLU ARG ARG ALA GLU PHE GLN ASP ILE ALA SEQRES 14 A 403 GLU ALA MET MET ARG VAL ASP GLN ASP ALA ALA ALA THR SEQRES 15 A 403 GLU ALA ALA GLY MET ARG LEU GLY GLY LEU LEU TYR GLN SEQRES 16 A 403 LEU VAL GLN GLU ARG ARG ALA ASN PRO GLY ASP ASP LEU SEQRES 17 A 403 ILE SER ALA LEU ILE THR THR GLU ASP PRO ASP GLY VAL SEQRES 18 A 403 VAL ASP ASP MET PHE LEU MET ASN ALA ALA GLY THR LEU SEQRES 19 A 403 LEU ILE ALA ALA HIS ASP THR THR ALA CYS MET ILE GLY SEQRES 20 A 403 LEU GLY THR ALA LEU LEU LEU ASP SER PRO ASP GLN LEU SEQRES 21 A 403 ALA LEU LEU ARG GLU ASP PRO SER LEU VAL GLY ASN ALA SEQRES 22 A 403 VAL GLU GLU LEU LEU ARG TYR LEU THR ILE GLY GLN PHE SEQRES 23 A 403 GLY GLY GLU ARG VAL ALA THR ARG ASP VAL GLU LEU GLY SEQRES 24 A 403 GLY VAL ARG ILE ALA LYS GLY GLU GLN VAL VAL ALA HIS SEQRES 25 A 403 VAL LEU ALA ALA ASP PHE ASP PRO ALA PHE VAL GLU GLU SEQRES 26 A 403 PRO GLU ARG PHE ASP ILE THR ARG ARG PRO ALA PRO HIS SEQRES 27 A 403 LEU ALA PHE GLY PHE GLY ALA HIS GLN CYS ILE GLY GLN SEQRES 28 A 403 GLN LEU ALA ARG ILE GLU LEU GLN ILE VAL PHE GLU THR SEQRES 29 A 403 LEU PHE ARG ARG LEU PRO GLY LEU ARG LEU ALA LYS PRO SEQRES 30 A 403 VAL GLU GLU LEU ARG PHE ARG HIS ASP MET VAL PHE TYR SEQRES 31 A 403 GLY VAL HIS GLU LEU PRO VAL THR TRP HIS HIS HIS HIS HET HEM A1408 43 HET FLI A 404 44 HET SO4 A 405 5 HET SO4 A 406 5 HET SO4 A 407 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM FLI (3R,4S,6S,8S,10R,12R,14R,16S,17E,19E,21E,23E,25E,28R)- HETNAM 2 FLI 3-HEXYL-4,6,8,10,12,14,16-HEPTAHYDROXY-17,28- HETNAM 3 FLI DIMETHYLOXACYCLOOCTACOSA-17,19,21,23,25-PENTAEN-2-ONE HETNAM SO4 SULFATE ION HETSYN HEM HEME HETSYN FLI FILIPIN I FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 FLI C35 H58 O9 FORMUL 4 SO4 3(O4 S 2-) FORMUL 7 HOH *592(H2 O) HELIX 1 1 GLY A 24 ALA A 32 1 9 HELIX 2 2 GLY A 50 ASP A 60 1 11 HELIX 3 3 PRO A 93 PHE A 106 1 14 HELIX 4 4 THR A 107 ALA A 113 1 7 HELIX 5 5 LEU A 114 GLY A 133 1 20 HELIX 6 6 LEU A 138 PHE A 142 1 5 HELIX 7 7 ASN A 144 GLY A 156 1 13 HELIX 8 8 PRO A 158 GLU A 160 5 3 HELIX 9 9 ARG A 161 MET A 173 1 13 HELIX 10 10 ASP A 178 ASN A 203 1 26 HELIX 11 11 ASP A 207 THR A 214 1 8 HELIX 12 12 ASP A 223 ASP A 255 1 33 HELIX 13 13 SER A 256 ASP A 266 1 11 HELIX 14 14 LEU A 269 THR A 282 1 14 HELIX 15 15 HIS A 312 ASP A 317 1 6 HELIX 16 16 PHE A 343 GLN A 347 5 5 HELIX 17 17 GLY A 350 LEU A 369 1 20 HELIX 18 18 PRO A 377 LEU A 381 5 5 SHEET 1 A 5 VAL A 34 THR A 38 0 SHEET 2 A 5 GLU A 44 VAL A 48 -1 O LEU A 47 N THR A 35 SHEET 3 A 5 GLN A 308 ALA A 311 1 O VAL A 310 N TRP A 46 SHEET 4 A 5 GLY A 288 ALA A 292 -1 N ARG A 290 O VAL A 309 SHEET 5 A 5 PHE A 63 SER A 64 -1 N SER A 64 O VAL A 291 SHEET 1 B 3 VAL A 136 ASP A 137 0 SHEET 2 B 3 PRO A 396 THR A 398 -1 O VAL A 397 N VAL A 136 SHEET 3 B 3 ARG A 373 LEU A 374 -1 N ARG A 373 O THR A 398 SHEET 1 C 2 VAL A 296 LEU A 298 0 SHEET 2 C 2 VAL A 301 ILE A 303 -1 O ILE A 303 N VAL A 296 LINK SG CYS A 348 FE HEM A1408 1555 1555 2.45 CISPEP 1 GLU A 92 PRO A 93 0 7.44 CISPEP 2 GLY A 134 PRO A 135 0 -1.07 SITE 1 AC1 22 LEU A 87 LEU A 88 HIS A 95 ARG A 99 SITE 2 AC1 22 PHE A 106 THR A 233 LEU A 234 ALA A 237 SITE 3 AC1 22 ALA A 238 THR A 241 ARG A 290 ALA A 340 SITE 4 AC1 22 PHE A 341 GLY A 342 ALA A 345 HIS A 346 SITE 5 AC1 22 CYS A 348 ILE A 349 GLY A 350 FLI A 404 SITE 6 AC1 22 HOH A 685 HOH A 823 SITE 1 AC2 22 GLN A 80 LYS A 81 PRO A 82 LEU A 88 SITE 2 AC2 22 THR A 182 GLY A 186 LEU A 189 GLY A 190 SITE 3 AC2 22 ASN A 229 ILE A 236 ALA A 237 GLY A 288 SITE 4 AC2 22 VAL A 313 VAL A 388 PHE A 389 HOH A 646 SITE 5 AC2 22 HOH A 664 HOH A 727 HOH A 761 HOH A 823 SITE 6 AC2 22 HOH A 857 HEM A1408 SITE 1 AC3 6 PRO A 12 LYS A 13 ALA A 14 HOH A 654 SITE 2 AC3 6 HOH A 787 HOH A 907 SITE 1 AC4 6 SER A 256 PRO A 257 ASP A 258 GLN A 259 SITE 2 AC4 6 HOH A 435 HOH A 554 SITE 1 AC5 4 PRO A 116 ARG A 120 HOH A 724 HOH A 763 CRYST1 91.368 91.368 151.239 90.00 90.00 90.00 P 41 21 2 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 0.010945 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010945 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006612 0.00000