HEADER OXIDOREDUCTASE 11-NOV-24 9EB0 TITLE CRYSTAL STRUCTURE OF THE FMN-BINDING DOMAIN OF HUMAN CYTOCHROME P450 TITLE 2 REDUCTASE (MUTANT D211N) 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 9EB0 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. 1.13 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 63780 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.140 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 1.1600 - 1.1300 0.78 3606 117 0.3028 0.3178 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) : 0.104 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.157 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.61 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 : 0.017 1499 REMARK 3 ANGLE : 1.462 2044 REMARK 3 CHIRALITY : 0.109 205 REMARK 3 PLANARITY : 0.015 269 REMARK 3 DIHEDRAL : 12.741 553 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 9EB0 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_1000289327. 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) : 0.9388 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 : 63981 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130 REMARK 200 RESOLUTION RANGE LOW (A) : 33.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 (%): 41.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.0, 0.075 M CALCIUM REMARK 280 CHLORIDE, 19% PEG 400, 5% 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 25.44200 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 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 -167.83 -118.92 REMARK 500 ASN A 178 115.73 -162.30 REMARK 500 LEU A 208 77.10 -116.95 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 A 644 DISTANCE = 6.65 ANGSTROMS 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 78.7 REMARK 620 3 HOH A 428 O 126.5 150.3 REMARK 620 4 HOH A 431 O 72.2 102.4 75.3 REMARK 620 5 HOH A 523 O 82.6 14.2 150.8 116.5 REMARK 620 6 HOH A 561 O 140.6 89.1 79.6 147.2 77.9 REMARK 620 7 HOH A 603 O 129.1 66.5 84.1 80.1 72.7 76.6 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B1C RELATED DB: PDB DBREF 9EB0 A 62 244 UNP P16435 NCPR_HUMAN 59 241 SEQADV 9EB0 MET A 60 UNP P16435 INITIATING METHIONINE SEQADV 9EB0 GLY A 61 UNP P16435 EXPRESSION TAG SEQADV 9EB0 ASN A 211 UNP P16435 ASP 208 ENGINEERED MUTATION SEQADV 9EB0 HIS A 245 UNP P16435 EXPRESSION TAG SEQADV 9EB0 HIS A 246 UNP P16435 EXPRESSION TAG SEQADV 9EB0 HIS A 247 UNP P16435 EXPRESSION TAG SEQADV 9EB0 HIS A 248 UNP P16435 EXPRESSION TAG SEQADV 9EB0 HIS A 249 UNP P16435 EXPRESSION TAG SEQADV 9EB0 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 HIS 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 ASN 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 *244(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 2.34 LINK O THR A 180 CA CA A 302 1555 1655 2.37 LINK CA CA A 302 O HOH A 428 1555 2545 2.43 LINK CA CA A 302 O HOH A 431 1555 2545 2.42 LINK CA CA A 302 O HOH A 523 1555 1555 2.21 LINK CA CA A 302 O HOH A 561 1555 1455 2.39 LINK CA CA A 302 O HOH A 603 1555 2545 2.38 CRYST1 39.155 50.884 47.195 90.00 106.08 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 0.025540 0.000000 0.007360 0.00000 SCALE2 0.000000 0.019653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022051 0.00000 CONECT 1566 2819 CONECT 2769 2770 2786 CONECT 2770 2769 2771 2772 CONECT 2771 2770 CONECT 2772 2770 2773 2800 CONECT 2773 2772 2774 2775 CONECT 2774 2773 CONECT 2775 2773 2776 2786 CONECT 2776 2775 2777 CONECT 2777 2776 2778 2784 CONECT 2778 2777 2779 2801 CONECT 2779 2778 2780 2781 CONECT 2780 2779 2802 2803 2804 CONECT 2781 2779 2782 2783 CONECT 2782 2781 2805 2806 2807 CONECT 2783 2781 2784 2808 CONECT 2784 2777 2783 2785 CONECT 2785 2784 2786 2787 CONECT 2786 2769 2775 2785 CONECT 2787 2785 2788 2809 2810 CONECT 2788 2787 2789 2790 2811 CONECT 2789 2788 2812 CONECT 2790 2788 2791 2792 2813 CONECT 2791 2790 2814 CONECT 2792 2790 2793 2794 2815 CONECT 2793 2792 2816 CONECT 2794 2792 2795 2817 2818 CONECT 2795 2794 2796 CONECT 2796 2795 2797 2798 2799 CONECT 2797 2796 CONECT 2798 2796 CONECT 2799 2796 CONECT 2800 2772 CONECT 2801 2778 CONECT 2802 2780 CONECT 2803 2780 CONECT 2804 2780 CONECT 2805 2782 CONECT 2806 2782 CONECT 2807 2782 CONECT 2808 2783 CONECT 2809 2787 CONECT 2810 2787 CONECT 2811 2788 CONECT 2812 2789 CONECT 2813 2790 CONECT 2814 2791 CONECT 2815 2792 CONECT 2816 2793 CONECT 2817 2794 CONECT 2818 2794 CONECT 2819 1566 2942 CONECT 2942 2819 MASTER 264 0 2 9 9 0 0 6 1617 1 53 15 END