HEADER OXIDOREDUCTASE 19-NOV-98 1B1C TITLE CRYSTAL STRUCTURE OF THE FMN-BINDING DOMAIN OF HUMAN CYTOCHROME P450 TITLE 2 REDUCTASE AT 1.93A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (NADPH-CYTOCHROME P450 REDUCTASE); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FMN-BINDING DOMAIN; COMPND 5 SYNONYM: P450R-FMN; COMPND 6 EC: 1.6.2.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 PLASMID: PMP CLONED INTO PET15B KEYWDS FLAVOPROTEIN, CYTOCHROME P450 REDUCTASE, P450 REDUCTASE, FMN-BINDING KEYWDS 2 DOMAIN, FMN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.ZHAO,S.MODI,G.SMITH,M.PAINE,P.D.MCDONAGH,C.R.WOLF,D.TEW,L.-Y.LIAN, AUTHOR 2 G.C.K.ROBERTS,H.P.C.DRIESSEN REVDAT 4 27-DEC-23 1B1C 1 REMARK LINK REVDAT 3 04-OCT-17 1B1C 1 REMARK REVDAT 2 24-FEB-09 1B1C 1 VERSN REVDAT 1 24-NOV-99 1B1C 0 JRNL AUTH Q.ZHAO,S.MODI,G.SMITH,M.PAINE,P.D.MCDONAGH,C.R.WOLF,D.TEW, JRNL AUTH 2 L.Y.LIAN,G.C.ROBERTS,H.P.DRIESSEN JRNL TITL CRYSTAL STRUCTURE OF THE FMN-BINDING DOMAIN OF HUMAN JRNL TITL 2 CYTOCHROME P450 REDUCTASE AT 1.93 A RESOLUTION. JRNL REF PROTEIN SCI. V. 8 298 1999 JRNL REFN ISSN 0961-8368 JRNL PMID 10048323 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Q.ZHAO,G.SMITH,S.MODI,M.PAINE,R.C.WOLF,D.TEW,L.Y.LIAN, REMARK 1 AUTH 2 W.U.PRIMROSE,G.C.ROBERTS,H.P.DRIESSEN REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION STUDIES OF REMARK 1 TITL 2 HUMAN CYTOCHROME P450 REDUCTASE REMARK 1 REF J.STRUCT.BIOL. V. 116 320 1996 REMARK 1 REFN ISSN 1047-8477 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 13282 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT, EXCEPT LAST 2 REMARK 3 PASSES REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1325 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.450 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.350 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-NOV-98. REMARK 100 THE DEPOSITION ID IS D_1000000114. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 287.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA, REMARK 200 TRUNCATE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13289 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 19.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 72.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: RSPS, VECREF REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18-20% (W/V) PEG400, 100 MM HEPES REMARK 280 (PH6.8-7.2), 200 MM CACL2 4 DEGREES C, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 25.72000 REMARK 290 SMTRY3 2 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 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 THR A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 VAL A 4 REMARK 465 ARG A 5 REMARK 465 GLU A 6 REMARK 465 VAL A 173 REMARK 465 GLU A 174 REMARK 465 ALA A 175 REMARK 465 THR A 176 REMARK 465 GLY A 177 REMARK 465 GLU A 178 REMARK 465 GLU A 179 REMARK 465 SER A 180 REMARK 465 SER A 181 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 TYR A 80 -168.12 -121.97 REMARK 500 GLU A 82 44.04 -93.07 REMARK 500 LYS A 116 -6.44 -58.77 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 CA A 200 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 104 OG REMARK 620 2 THR A 117 O 82.6 REMARK 620 3 HOH A 201 O 139.4 77.7 REMARK 620 4 HOH A 237 O 122.7 154.4 83.4 REMARK 620 5 HOH A 279 O 77.4 109.2 76.2 82.4 REMARK 620 6 HOH A 280 O 129.7 74.8 78.3 84.6 152.5 REMARK 620 7 HOH A 281 O 67.8 112.8 152.8 77.8 119.8 80.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 190 DBREF 1B1C A 1 181 UNP P16435 NCPR_HUMAN 61 241 SEQRES 1 A 181 THR SER SER VAL ARG GLU SER SER PHE VAL GLU LYS MET SEQRES 2 A 181 LYS LYS THR GLY ARG ASN ILE ILE VAL PHE TYR GLY SER SEQRES 3 A 181 GLN THR GLY THR ALA GLU GLU PHE ALA ASN ARG LEU SER SEQRES 4 A 181 LYS ASP ALA HIS ARG TYR GLY MET ARG GLY MET SER ALA SEQRES 5 A 181 ASP PRO GLU GLU TYR ASP LEU ALA ASP LEU SER SER LEU SEQRES 6 A 181 PRO GLU ILE ASP ASN ALA LEU VAL VAL PHE CYS MET ALA SEQRES 7 A 181 THR TYR GLY GLU GLY ASP PRO THR ASP ASN ALA GLN ASP SEQRES 8 A 181 PHE TYR ASP TRP LEU GLN GLU THR ASP VAL ASP LEU SER SEQRES 9 A 181 GLY VAL LYS PHE ALA VAL PHE GLY LEU GLY ASN LYS THR SEQRES 10 A 181 TYR GLU HIS PHE ASN ALA MET GLY LYS TYR VAL ASP LYS SEQRES 11 A 181 ARG LEU GLU GLN LEU GLY ALA GLN ARG ILE PHE GLU LEU SEQRES 12 A 181 GLY LEU GLY ASP ASP ASP GLY ASN LEU GLU GLU ASP PHE SEQRES 13 A 181 ILE THR TRP ARG GLU GLN PHE TRP PRO ALA VAL CYS GLU SEQRES 14 A 181 HIS PHE GLY VAL GLU ALA THR GLY GLU GLU SER SER HET CA A 200 1 HET FMN A 190 31 HETNAM CA CALCIUM ION HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 CA CA 2+ FORMUL 3 FMN C17 H21 N4 O9 P FORMUL 4 HOH *61(H2 O) HELIX 1 A1 PHE A 9 LYS A 15 1 7 HELIX 2 A2 THR A 30 ASP A 41 1 12 HELIX 3 A2 ALA A 42 TYR A 45 5 4 HELIX 4 A3 PRO A 54 GLU A 56 5 3 HELIX 5 A4 LEU A 59 GLU A 67 5 9 HELIX 6 A5 ASP A 87 ALA A 89 5 3 HELIX 7 A5 GLN A 90 GLU A 98 1 9 HELIX 8 A6 ALA A 123 GLN A 134 1 12 HELIX 9 A7 LEU A 152 PHE A 171 1 20 SHEET 1 B1 1 ILE A 20 GLY A 25 0 SHEET 1 B2 1 GLY A 49 ALA A 52 0 SHEET 1 B3 1 LEU A 72 ALA A 78 0 SHEET 1 B4 1 LYS A 107 GLY A 114 0 SHEET 1 B5A 1 GLN A 138 ARG A 139 0 SHEET 1 B5B 1 GLY A 144 ASP A 147 0 LINK OG SER A 104 CA CA A 200 1555 1555 2.21 LINK O THR A 117 CA CA A 200 1455 1555 2.34 LINK CA CA A 200 O HOH A 201 1555 1555 2.35 LINK CA CA A 200 O HOH A 237 1555 1555 2.30 LINK CA CA A 200 O HOH A 279 1555 1555 2.32 LINK CA CA A 200 O HOH A 280 1555 1555 2.46 LINK CA CA A 200 O HOH A 281 1555 1555 2.32 SITE 1 AC1 7 SER A 104 THR A 117 HOH A 201 HOH A 237 SITE 2 AC1 7 HOH A 279 HOH A 280 HOH A 281 SITE 1 AC2 22 SER A 26 GLN A 27 THR A 28 GLY A 29 SITE 2 AC2 22 THR A 30 ALA A 31 GLU A 67 ALA A 78 SITE 3 AC2 22 THR A 79 TYR A 80 GLY A 81 LEU A 113 SITE 4 AC2 22 GLY A 114 ASN A 115 TYR A 118 HIS A 120 SITE 5 AC2 22 PHE A 121 ASN A 122 ASP A 148 LEU A 152 SITE 6 AC2 22 HOH A 241 HOH A 278 CRYST1 39.310 51.440 47.600 90.00 105.93 90.00 P 1 21 1 2 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 0.025439 0.000000 0.007261 0.00000 SCALE2 0.000000 0.019440 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021847 0.00000