HEADER OXIDOREDUCTASE 11-NOV-24 9EAY TITLE CRYSTAL STRUCTURE OF THE FMN-BINDING DOMAIN OF HUMAN CYTOCHROME P450 TITLE 2 REDUCTASE (MUTANT H183Y) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADPH--CYTOCHROME P450 REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CPR,P450R; COMPND 5 EC: 1.6.2.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POR, CYPOR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C41 KEYWDS CYTOCHROME P450 FMN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.D.BURRIS-HIDAY,E.E.SCOTT REVDAT 1 17-JUN-26 9EAY 0 JRNL AUTH S.D.BURRIS-HIDAY,E.E.SCOTT JRNL TITL STRUCTURAL INSIGHTS INTO MUTANT FORMS OF HUMAN NADPH JRNL TITL 2 CYTOCHROME P450 REDUCTASE FMN CONTAINING DOMAIN VIA X-RAY JRNL TITL 3 CRYSTALLOGRAPHY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21_5207 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 27606 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.240 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.5000 - 2.2800 1.00 1848 144 0.1558 0.1896 REMARK 3 2 1.5400 - 1.5000 0.93 1703 133 0.3428 0.3779 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.177 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.632 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.41 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1398 REMARK 3 ANGLE : 0.913 1893 REMARK 3 CHIRALITY : 0.077 190 REMARK 3 PLANARITY : 0.009 247 REMARK 3 DIHEDRAL : 14.734 498 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9EAY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1000289320. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27784 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 37.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: NULL REMARK 200 REMARK 200 REMARK: THIN PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.0, 0.05 M CALCIUM REMARK 280 CHLORIDE, 19% PEG 400, 20% GLYCEROL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295K 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 25.40750 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 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 60 REMARK 465 GLY A 61 REMARK 465 THR A 62 REMARK 465 LEU A 63 REMARK 465 THR A 64 REMARK 465 SER A 65 REMARK 465 SER A 66 REMARK 465 VAL A 67 REMARK 465 ARG A 68 REMARK 465 GLU A 69 REMARK 465 GLU A 237 REMARK 465 ALA A 238 REMARK 465 THR A 239 REMARK 465 GLY A 240 REMARK 465 GLU A 241 REMARK 465 GLU A 242 REMARK 465 SER A 243 REMARK 465 SER A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 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 143 -169.00 -119.24 REMARK 500 ASN A 178 114.91 -160.45 REMARK 500 TYR A 183 68.15 -100.93 REMARK 500 LEU A 208 76.73 -116.53 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 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 167 OG REMARK 620 2 THR A 180 O 79.7 REMARK 620 3 HOH A 413 O 150.2 98.7 REMARK 620 4 HOH A 439 O 82.0 18.0 88.0 REMARK 620 5 HOH A 485 O 132.9 144.4 60.8 145.0 REMARK 620 6 HOH A 502 O 115.1 55.4 86.5 68.6 92.5 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B1C RELATED DB: PDB DBREF 9EAY A 62 244 UNP P16435 NCPR_HUMAN 59 241 SEQADV 9EAY MET A 60 UNP P16435 INITIATING METHIONINE SEQADV 9EAY GLY A 61 UNP P16435 EXPRESSION TAG SEQADV 9EAY TYR A 183 UNP P16435 HIS 180 ENGINEERED MUTATION SEQADV 9EAY HIS A 245 UNP P16435 EXPRESSION TAG SEQADV 9EAY HIS A 246 UNP P16435 EXPRESSION TAG SEQADV 9EAY HIS A 247 UNP P16435 EXPRESSION TAG SEQADV 9EAY HIS A 248 UNP P16435 EXPRESSION TAG SEQADV 9EAY HIS A 249 UNP P16435 EXPRESSION TAG SEQADV 9EAY HIS A 250 UNP P16435 EXPRESSION TAG SEQRES 1 A 191 MET GLY THR LEU THR SER SER VAL ARG GLU SER SER PHE SEQRES 2 A 191 VAL GLU LYS MET LYS LYS THR GLY ARG ASN ILE ILE VAL SEQRES 3 A 191 PHE TYR GLY SER GLN THR GLY THR ALA GLU GLU PHE ALA SEQRES 4 A 191 ASN ARG LEU SER LYS ASP ALA HIS ARG TYR GLY MET ARG SEQRES 5 A 191 GLY MET SER ALA ASP PRO GLU GLU TYR ASP LEU ALA ASP SEQRES 6 A 191 LEU SER SER LEU PRO GLU ILE ASP ASN ALA LEU VAL VAL SEQRES 7 A 191 PHE CYS MET ALA THR TYR GLY GLU GLY ASP PRO THR ASP SEQRES 8 A 191 ASN ALA GLN ASP PHE TYR ASP TRP LEU GLN GLU THR ASP SEQRES 9 A 191 VAL ASP LEU SER GLY VAL LYS PHE ALA VAL PHE GLY LEU SEQRES 10 A 191 GLY ASN LYS THR TYR GLU TYR PHE ASN ALA MET GLY LYS SEQRES 11 A 191 TYR VAL ASP LYS ARG LEU GLU GLN LEU GLY ALA GLN ARG SEQRES 12 A 191 ILE PHE GLU LEU GLY LEU GLY ASP ASP ASP GLY ASN LEU SEQRES 13 A 191 GLU GLU ASP PHE ILE THR TRP ARG GLU GLN PHE TRP PRO SEQRES 14 A 191 ALA VAL CYS GLU HIS PHE GLY VAL GLU ALA THR GLY GLU SEQRES 15 A 191 GLU SER SER HIS HIS HIS HIS HIS HIS HET FMN A 301 50 HET CA A 302 1 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM CA CALCIUM ION HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 CA CA 2+ FORMUL 4 HOH *112(H2 O) HELIX 1 AA1 SER A 71 GLY A 80 1 10 HELIX 2 AA2 GLY A 92 ALA A 105 1 14 HELIX 3 AA3 HIS A 106 GLY A 109 5 4 HELIX 4 AA4 ASP A 116 TYR A 120 5 5 HELIX 5 AA5 ASP A 121 ILE A 131 5 11 HELIX 6 AA6 GLY A 144 GLY A 146 5 3 HELIX 7 AA7 ALA A 152 THR A 162 1 11 HELIX 8 AA8 ASN A 185 LEU A 198 1 14 HELIX 9 AA9 ASN A 214 GLY A 235 1 22 SHEET 1 AA1 5 GLY A 112 ALA A 115 0 SHEET 2 AA1 5 ILE A 83 GLY A 88 1 N VAL A 85 O MET A 113 SHEET 3 AA1 5 LEU A 135 TYR A 143 1 O CYS A 139 N PHE A 86 SHEET 4 AA1 5 LYS A 170 GLY A 177 1 O PHE A 174 N PHE A 138 SHEET 5 AA1 5 GLN A 201 ARG A 202 1 O GLN A 201 N PHE A 171 SHEET 1 AA2 4 ASP A 147 PRO A 148 0 SHEET 2 AA2 4 LEU A 135 TYR A 143 -1 N TYR A 143 O ASP A 147 SHEET 3 AA2 4 LYS A 170 GLY A 177 1 O PHE A 174 N PHE A 138 SHEET 4 AA2 4 GLY A 207 ASP A 210 1 O GLY A 207 N GLY A 175 LINK OG SER A 167 CA CA A 302 1555 1555 2.49 LINK O THR A 180 CA CA A 302 1555 1655 2.36 LINK CA CA A 302 O HOH A 413 1555 1455 2.02 LINK CA CA A 302 O HOH A 439 1555 1555 2.22 LINK CA CA A 302 O HOH A 485 1555 1455 2.40 LINK CA CA A 302 O HOH A 502 1555 2545 2.31 CRYST1 39.005 50.815 46.666 90.00 107.08 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 0.025638 0.000000 0.007876 0.00000 SCALE2 0.000000 0.019679 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022417 0.00000 CONECT 1475 2622 CONECT 2572 2573 2589 CONECT 2573 2572 2574 2575 CONECT 2574 2573 CONECT 2575 2573 2576 2603 CONECT 2576 2575 2577 2578 CONECT 2577 2576 CONECT 2578 2576 2579 2589 CONECT 2579 2578 2580 CONECT 2580 2579 2581 2587 CONECT 2581 2580 2582 2604 CONECT 2582 2581 2583 2584 CONECT 2583 2582 2605 2606 2607 CONECT 2584 2582 2585 2586 CONECT 2585 2584 2608 2609 2610 CONECT 2586 2584 2587 2611 CONECT 2587 2580 2586 2588 CONECT 2588 2587 2589 2590 CONECT 2589 2572 2578 2588 CONECT 2590 2588 2591 2612 2613 CONECT 2591 2590 2592 2593 2614 CONECT 2592 2591 2615 CONECT 2593 2591 2594 2595 2616 CONECT 2594 2593 2617 CONECT 2595 2593 2596 2597 2618 CONECT 2596 2595 2619 CONECT 2597 2595 2598 2620 2621 CONECT 2598 2597 2599 CONECT 2599 2598 2600 2601 2602 CONECT 2600 2599 CONECT 2601 2599 CONECT 2602 2599 CONECT 2603 2575 CONECT 2604 2581 CONECT 2605 2583 CONECT 2606 2583 CONECT 2607 2583 CONECT 2608 2585 CONECT 2609 2585 CONECT 2610 2585 CONECT 2611 2586 CONECT 2612 2590 CONECT 2613 2590 CONECT 2614 2591 CONECT 2615 2592 CONECT 2616 2593 CONECT 2617 2594 CONECT 2618 2595 CONECT 2619 2596 CONECT 2620 2597 CONECT 2621 2597 CONECT 2622 1475 2661 CONECT 2661 2622 MASTER 253 0 2 9 9 0 0 6 1478 1 53 15 END