PDB Short entry for 3DL9 HEADER OXIDOREDUCTASE 26-JUN-08 3DL9 TITLE CRYSTAL STRUCTURE OF CYP2R1 IN COMPLEX WITH 1-ALPHA-HYDROXY-VITAMIN D2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 2R1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: VITAMIN D 25-HYDROXYLASE; COMPND 5 EC: 1.14.14.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: CYP2R1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCW KEYWDS CYTOCHROME P450, VITAMIN D, VITAMIN S 25-HYDROXYLASE, DRUG KEYWDS 2 METABOLISM, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 3 SGC, DISEASE MUTATION, ENDOPLASMIC RETICULUM, HEME, IRON, MEMBRANE, KEYWDS 4 METAL-BINDING, MICROSOME, MONOOXYGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.V.STRUSHKEVICH,W.TEMPEL,A.A.GILEP,P.LOPPNAU,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,C.BOUNTRA,M.WILKSTROM,A.BOCHKAREV,H.PARK,STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (SGC) REVDAT 5 30-AUG-23 3DL9 1 HETSYN REVDAT 4 29-JUL-20 3DL9 1 COMPND REMARK SEQADV HET REVDAT 4 2 1 HETNAM HETSYN FORMUL LINK REVDAT 4 3 1 SITE ATOM REVDAT 3 25-OCT-17 3DL9 1 REMARK REVDAT 2 24-FEB-09 3DL9 1 VERSN REVDAT 1 05-AUG-08 3DL9 0 JRNL AUTH N.V.STRUSHKEVICH,W.TEMPEL,A.A.GILEP,P.LOPPNAU, JRNL AUTH 2 C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,M.WILKSTROM, JRNL AUTH 3 A.BOCHKAREV,H.PARK JRNL TITL CRYSTAL STRUCTURE OF CYP2R1 IN COMPLEX WITH JRNL TITL 2 1-ALPHA-HYDROXY-VITAMIN D2. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0037 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) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 45761 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS (SFTOOLS) REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.992 REMARK 3 FREE R VALUE TEST SET COUNT : 1369 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) : 2.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3196 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7453 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 300 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.83700 REMARK 3 B22 (A**2) : -2.16300 REMARK 3 B33 (A**2) : -1.67500 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): 0.402 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.254 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.201 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.350 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8106 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 5421 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11097 ; 1.392 ; 2.048 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13168 ; 1.019 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 930 ; 5.462 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 366 ;33.272 ;23.470 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1218 ;14.219 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;22.841 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1204 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8795 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1696 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1860 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 5604 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4055 ; 0.186 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3844 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 213 ; 0.146 ; 0.200 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): 16 ; 0.176 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 37 ; 0.284 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.085 ; 0.200 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): 4836 ; 1.331 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1867 ; 0.198 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7525 ; 2.171 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3826 ; 1.035 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3564 ; 1.555 ; 3.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. PROGRAMS COOT, PRODRG, MOLPROBITY HAVE ALSO REMARK 3 BEEN USED IN REFINEMENT. 3. THE 2-HYDROXYPROPYL-BETA- REMARK 3 CYCLODEXTRIN WAS ADDED TO THE PROTEIN SAMPLE. DUE TO LIMITED REMARK 3 RESOLUTION OF THE ELECTRON DENSITY MAP AND LACK OF A PRECISE REMARK 3 CHEMICAL DESCRIPTION OF THE ADDITIVE, IT WAS MODELED HERE AS REMARK 3 BETA-CYCLODEXTRIN. REMARK 4 REMARK 4 3DL9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46055 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.720 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.16300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.95700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.3.0037 REMARK 200 STARTING MODEL: PDB ENTRY 3CZH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M AMMOUNIUM SULFATE, 0.1M ADA, PH REMARK 280 6.5, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 76.29400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.29400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 68.65150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 81.52000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 68.65150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 81.52000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 76.29400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 68.65150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 81.52000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 76.29400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 68.65150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 81.52000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS REMARK 300 UNKNOWN. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 27 REMARK 465 ALA A 28 REMARK 465 LYS A 29 REMARK 465 LYS A 30 REMARK 465 THR A 31 REMARK 465 LYS A 32 REMARK 465 GLN A 33 REMARK 465 ARG A 34 REMARK 465 ARG A 35 REMARK 465 PRO A 36 REMARK 465 MET A 37 REMARK 465 HIS A 503 REMARK 465 HIS A 504 REMARK 465 HIS A 505 REMARK 465 MET B 27 REMARK 465 ALA B 28 REMARK 465 LYS B 29 REMARK 465 LYS B 30 REMARK 465 THR B 31 REMARK 465 LYS B 32 REMARK 465 GLN B 33 REMARK 465 ARG B 34 REMARK 465 ARG B 35 REMARK 465 PRO B 36 REMARK 465 MET B 37 REMARK 465 GLY B 38 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 LYS A 120 CE NZ REMARK 470 LYS A 152 CG CD CE NZ REMARK 470 LYS A 163 CD CE NZ REMARK 470 ARG A 175 NE CZ NH1 NH2 REMARK 470 ARG A 248 NE CZ NH1 NH2 REMARK 470 LYS A 269 CD CE NZ REMARK 470 GLN A 271 CD OE1 NE2 REMARK 470 LYS A 297 CD CE NZ REMARK 470 LYS A 349 CG CD CE NZ REMARK 470 LYS A 357 CE NZ REMARK 470 ARG A 415 CD NE CZ NH1 NH2 REMARK 470 LYS A 434 CE NZ REMARK 470 LEU A 477 CD1 CD2 REMARK 470 ARG A 500 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 60 CG CD OE1 OE2 REMARK 470 SER B 85 OG REMARK 470 LYS B 96 CE NZ REMARK 470 LYS B 120 CE NZ REMARK 470 ARG B 145 NE CZ NH1 NH2 REMARK 470 LYS B 152 CG CD CE NZ REMARK 470 LYS B 163 CE NZ REMARK 470 ARG B 175 NE CZ NH1 NH2 REMARK 470 GLU B 203 CD OE1 OE2 REMARK 470 GLU B 262 CG CD OE1 OE2 REMARK 470 GLN B 271 CG CD OE1 NE2 REMARK 470 LYS B 288 CG CD CE NZ REMARK 470 LYS B 297 CD CE NZ REMARK 470 GLU B 298 CG CD OE1 OE2 REMARK 470 LYS B 349 CD CE NZ REMARK 470 LYS B 357 CE NZ REMARK 470 ARG B 415 CD NE CZ NH1 NH2 REMARK 470 SER B 428 OG REMARK 470 LYS B 434 CG CD CE NZ 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 ARG A 446 NE - CZ - NH2 ANGL. DEV. = -3.1 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 PHE A 48 -68.12 75.82 REMARK 500 LEU A 124 -63.49 -123.29 REMARK 500 ASP A 204 74.52 -69.75 REMARK 500 GLN A 271 8.71 54.32 REMARK 500 HIS A 275 -178.81 -172.58 REMARK 500 ASN A 373 77.46 49.93 REMARK 500 LYS A 396 131.62 -36.60 REMARK 500 HIS A 421 83.32 -161.29 REMARK 500 VAL A 439 52.92 -140.81 REMARK 500 SER A 442 -172.93 62.30 REMARK 500 GLU A 476 27.44 46.27 REMARK 500 PHE B 48 -69.72 78.60 REMARK 500 VAL B 100 -62.15 -94.35 REMARK 500 LEU B 124 -67.69 -134.50 REMARK 500 GLN B 271 -15.68 72.18 REMARK 500 ALA B 437 30.95 -80.25 REMARK 500 VAL B 439 49.03 -145.61 REMARK 500 SER B 442 -169.03 74.42 REMARK 500 GLU B 476 38.36 39.03 REMARK 500 ARG B 501 -78.70 -84.86 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 A 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 448 SG REMARK 620 2 HEM A 601 NA 97.8 REMARK 620 3 HEM A 601 NB 87.7 88.7 REMARK 620 4 HEM A 601 NC 87.1 174.8 89.8 REMARK 620 5 HEM A 601 ND 97.4 90.1 174.8 91.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 448 SG REMARK 620 2 HEM A 601 NA 110.0 REMARK 620 3 HEM A 601 NB 100.8 82.2 REMARK 620 4 HEM A 601 NC 103.6 146.1 87.3 REMARK 620 5 HEM A 601 ND 112.6 83.2 146.4 88.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 448 SG REMARK 620 2 HEM B 601 NA 107.4 REMARK 620 3 HEM B 601 NB 87.6 81.6 REMARK 620 4 HEM B 601 NC 93.4 155.8 87.2 REMARK 620 5 HEM B 601 ND 114.4 90.0 157.9 92.6 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CZH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CYP2R1 IN COMPLEX WITH VITAMIN D2 DBREF 3DL9 A 32 501 UNP Q6VVX0 CP2R1_HUMAN 32 501 DBREF 3DL9 B 32 501 UNP Q6VVX0 CP2R1_HUMAN 32 501 SEQADV 3DL9 MET A 27 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 ALA A 28 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 LYS A 29 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 LYS A 30 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 THR A 31 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 HIS A 502 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 HIS A 503 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 HIS A 504 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 HIS A 505 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 MET B 27 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 ALA B 28 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 LYS B 29 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 LYS B 30 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 THR B 31 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 HIS B 502 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 HIS B 503 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 HIS B 504 UNP Q6VVX0 EXPRESSION TAG SEQADV 3DL9 HIS B 505 UNP Q6VVX0 EXPRESSION TAG SEQRES 1 A 479 MET ALA LYS LYS THR LYS GLN ARG ARG PRO MET GLY PHE SEQRES 2 A 479 PRO PRO GLY PRO PRO GLY LEU PRO PHE ILE GLY ASN ILE SEQRES 3 A 479 TYR SER LEU ALA ALA SER SER GLU LEU PRO HIS VAL TYR SEQRES 4 A 479 MET ARG LYS GLN SER GLN VAL TYR GLY GLU ILE PHE SER SEQRES 5 A 479 LEU ASP LEU GLY GLY ILE SER THR VAL VAL LEU ASN GLY SEQRES 6 A 479 TYR ASP VAL VAL LYS GLU CYS LEU VAL HIS GLN SER GLU SEQRES 7 A 479 ILE PHE ALA ASP ARG PRO CYS LEU PRO LEU PHE MET LYS SEQRES 8 A 479 MET THR LYS MET GLY GLY LEU LEU ASN SER ARG TYR GLY SEQRES 9 A 479 ARG GLY TRP VAL ASP HIS ARG ARG LEU ALA VAL ASN SER SEQRES 10 A 479 PHE ARG TYR PHE GLY TYR GLY GLN LYS SER PHE GLU SER SEQRES 11 A 479 LYS ILE LEU GLU GLU THR LYS PHE PHE ASN ASP ALA ILE SEQRES 12 A 479 GLU THR TYR LYS GLY ARG PRO PHE ASP PHE LYS GLN LEU SEQRES 13 A 479 ILE THR ASN ALA VAL SER ASN ILE THR ASN LEU ILE ILE SEQRES 14 A 479 PHE GLY GLU ARG PHE THR TYR GLU ASP THR ASP PHE GLN SEQRES 15 A 479 HIS MET ILE GLU LEU PHE SER GLU ASN VAL GLU LEU ALA SEQRES 16 A 479 ALA SER ALA SER VAL PHE LEU TYR ASN ALA PHE PRO TRP SEQRES 17 A 479 ILE GLY ILE LEU PRO PHE GLY LYS HIS GLN GLN LEU PHE SEQRES 18 A 479 ARG ASN ALA ALA VAL VAL TYR ASP PHE LEU SER ARG LEU SEQRES 19 A 479 ILE GLU LYS ALA SER VAL ASN ARG LYS PRO GLN LEU PRO SEQRES 20 A 479 GLN HIS PHE VAL ASP ALA TYR LEU ASP GLU MET ASP GLN SEQRES 21 A 479 GLY LYS ASN ASP PRO SER SER THR PHE SER LYS GLU ASN SEQRES 22 A 479 LEU ILE PHE SER VAL GLY GLU LEU ILE ILE ALA GLY THR SEQRES 23 A 479 GLU THR THR THR ASN VAL LEU ARG TRP ALA ILE LEU PHE SEQRES 24 A 479 MET ALA LEU TYR PRO ASN ILE GLN GLY GLN VAL GLN LYS SEQRES 25 A 479 GLU ILE ASP LEU ILE MET GLY PRO ASN GLY LYS PRO SER SEQRES 26 A 479 TRP ASP ASP LYS CYS LYS MET PRO TYR THR GLU ALA VAL SEQRES 27 A 479 LEU HIS GLU VAL LEU ARG PHE CYS ASN ILE VAL PRO LEU SEQRES 28 A 479 GLY ILE PHE HIS ALA THR SER GLU ASP ALA VAL VAL ARG SEQRES 29 A 479 GLY TYR SER ILE PRO LYS GLY THR THR VAL ILE THR ASN SEQRES 30 A 479 LEU TYR SER VAL HIS PHE ASP GLU LYS TYR TRP ARG ASP SEQRES 31 A 479 PRO GLU VAL PHE HIS PRO GLU ARG PHE LEU ASP SER SER SEQRES 32 A 479 GLY TYR PHE ALA LYS LYS GLU ALA LEU VAL PRO PHE SER SEQRES 33 A 479 LEU GLY ARG ARG HIS CYS LEU GLY GLU HIS LEU ALA ARG SEQRES 34 A 479 MET GLU MET PHE LEU PHE PHE THR ALA LEU LEU GLN ARG SEQRES 35 A 479 PHE HIS LEU HIS PHE PRO HIS GLU LEU VAL PRO ASP LEU SEQRES 36 A 479 LYS PRO ARG LEU GLY MET THR LEU GLN PRO GLN PRO TYR SEQRES 37 A 479 LEU ILE CYS ALA GLU ARG ARG HIS HIS HIS HIS SEQRES 1 B 479 MET ALA LYS LYS THR LYS GLN ARG ARG PRO MET GLY PHE SEQRES 2 B 479 PRO PRO GLY PRO PRO GLY LEU PRO PHE ILE GLY ASN ILE SEQRES 3 B 479 TYR SER LEU ALA ALA SER SER GLU LEU PRO HIS VAL TYR SEQRES 4 B 479 MET ARG LYS GLN SER GLN VAL TYR GLY GLU ILE PHE SER SEQRES 5 B 479 LEU ASP LEU GLY GLY ILE SER THR VAL VAL LEU ASN GLY SEQRES 6 B 479 TYR ASP VAL VAL LYS GLU CYS LEU VAL HIS GLN SER GLU SEQRES 7 B 479 ILE PHE ALA ASP ARG PRO CYS LEU PRO LEU PHE MET LYS SEQRES 8 B 479 MET THR LYS MET GLY GLY LEU LEU ASN SER ARG TYR GLY SEQRES 9 B 479 ARG GLY TRP VAL ASP HIS ARG ARG LEU ALA VAL ASN SER SEQRES 10 B 479 PHE ARG TYR PHE GLY TYR GLY GLN LYS SER PHE GLU SER SEQRES 11 B 479 LYS ILE LEU GLU GLU THR LYS PHE PHE ASN ASP ALA ILE SEQRES 12 B 479 GLU THR TYR LYS GLY ARG PRO PHE ASP PHE LYS GLN LEU SEQRES 13 B 479 ILE THR ASN ALA VAL SER ASN ILE THR ASN LEU ILE ILE SEQRES 14 B 479 PHE GLY GLU ARG PHE THR TYR GLU ASP THR ASP PHE GLN SEQRES 15 B 479 HIS MET ILE GLU LEU PHE SER GLU ASN VAL GLU LEU ALA SEQRES 16 B 479 ALA SER ALA SER VAL PHE LEU TYR ASN ALA PHE PRO TRP SEQRES 17 B 479 ILE GLY ILE LEU PRO PHE GLY LYS HIS GLN GLN LEU PHE SEQRES 18 B 479 ARG ASN ALA ALA VAL VAL TYR ASP PHE LEU SER ARG LEU SEQRES 19 B 479 ILE GLU LYS ALA SER VAL ASN ARG LYS PRO GLN LEU PRO SEQRES 20 B 479 GLN HIS PHE VAL ASP ALA TYR LEU ASP GLU MET ASP GLN SEQRES 21 B 479 GLY LYS ASN ASP PRO SER SER THR PHE SER LYS GLU ASN SEQRES 22 B 479 LEU ILE PHE SER VAL GLY GLU LEU ILE ILE ALA GLY THR SEQRES 23 B 479 GLU THR THR THR ASN VAL LEU ARG TRP ALA ILE LEU PHE SEQRES 24 B 479 MET ALA LEU TYR PRO ASN ILE GLN GLY GLN VAL GLN LYS SEQRES 25 B 479 GLU ILE ASP LEU ILE MET GLY PRO ASN GLY LYS PRO SER SEQRES 26 B 479 TRP ASP ASP LYS CYS LYS MET PRO TYR THR GLU ALA VAL SEQRES 27 B 479 LEU HIS GLU VAL LEU ARG PHE CYS ASN ILE VAL PRO LEU SEQRES 28 B 479 GLY ILE PHE HIS ALA THR SER GLU ASP ALA VAL VAL ARG SEQRES 29 B 479 GLY TYR SER ILE PRO LYS GLY THR THR VAL ILE THR ASN SEQRES 30 B 479 LEU TYR SER VAL HIS PHE ASP GLU LYS TYR TRP ARG ASP SEQRES 31 B 479 PRO GLU VAL PHE HIS PRO GLU ARG PHE LEU ASP SER SER SEQRES 32 B 479 GLY TYR PHE ALA LYS LYS GLU ALA LEU VAL PRO PHE SER SEQRES 33 B 479 LEU GLY ARG ARG HIS CYS LEU GLY GLU HIS LEU ALA ARG SEQRES 34 B 479 MET GLU MET PHE LEU PHE PHE THR ALA LEU LEU GLN ARG SEQRES 35 B 479 PHE HIS LEU HIS PHE PRO HIS GLU LEU VAL PRO ASP LEU SEQRES 36 B 479 LYS PRO ARG LEU GLY MET THR LEU GLN PRO GLN PRO TYR SEQRES 37 B 479 LEU ILE CYS ALA GLU ARG ARG HIS HIS HIS HIS HET GLC C 1 11 HET GLC C 2 11 HET GLC C 3 11 HET GLC C 4 11 HET GLC C 5 11 HET GLC C 6 11 HET GLC C 7 11 HET GLC D 1 11 HET GLC D 2 11 HET GLC D 3 11 HET GLC D 4 11 HET GLC D 5 11 HET GLC D 6 11 HET GLC D 7 11 HET HEM A 601 86 HET V2H A 602 30 HET HEM B 601 86 HET V2H B 602 30 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM V2H (1S,3R,5Z,7E,22E)-9,10-SECOERGOSTA-5,7,10,22-TETRAENE- HETNAM 2 V2H 1,3-DIOL HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN HEM HEME HETSYN V2H 1-ALPHA-HYDROXY-VITAMIN D2 FORMUL 3 GLC 14(C6 H12 O6) FORMUL 5 HEM 2(C34 H32 FE N4 O4) FORMUL 6 V2H 2(C28 H44 O2) FORMUL 9 HOH *120(H2 O) HELIX 1 1 ASN A 51 SER A 58 1 8 HELIX 2 2 LEU A 61 GLY A 74 1 14 HELIX 3 3 GLY A 91 VAL A 100 1 10 HELIX 4 4 LEU A 112 LYS A 120 1 9 HELIX 5 5 GLY A 130 GLY A 148 1 19 HELIX 6 6 SER A 153 THR A 171 1 19 HELIX 7 7 PHE A 179 GLY A 197 1 19 HELIX 8 8 ASP A 204 ALA A 221 1 18 HELIX 9 9 SER A 223 PHE A 232 1 10 HELIX 10 10 PRO A 233 LEU A 238 5 6 HELIX 11 11 GLY A 241 VAL A 266 1 26 HELIX 12 12 HIS A 275 GLY A 287 1 13 HELIX 13 13 SER A 296 TYR A 329 1 34 HELIX 14 14 TYR A 329 GLY A 345 1 17 HELIX 15 15 SER A 351 LYS A 357 5 7 HELIX 16 16 MET A 358 ASN A 373 1 16 HELIX 17 17 LEU A 404 PHE A 409 1 6 HELIX 18 18 HIS A 421 LEU A 426 5 6 HELIX 19 19 GLY A 450 ARG A 468 1 19 HELIX 20 20 PHE A 473 LEU A 477 5 5 HELIX 21 21 ASN B 51 ALA B 57 1 7 HELIX 22 22 LEU B 61 GLY B 74 1 14 HELIX 23 23 ASN B 90 VAL B 100 1 11 HELIX 24 24 LEU B 112 LYS B 120 1 9 HELIX 25 25 GLY B 130 PHE B 147 1 18 HELIX 26 26 SER B 153 THR B 171 1 19 HELIX 27 27 PHE B 179 GLY B 197 1 19 HELIX 28 28 ASP B 204 ALA B 221 1 18 HELIX 29 29 SER B 223 PHE B 232 1 10 HELIX 30 30 PRO B 233 LEU B 238 5 6 HELIX 31 31 LYS B 242 ALA B 264 1 23 HELIX 32 32 HIS B 275 GLN B 286 1 12 HELIX 33 33 SER B 296 TYR B 329 1 34 HELIX 34 34 TYR B 329 MET B 344 1 16 HELIX 35 35 SER B 351 LYS B 357 5 7 HELIX 36 36 MET B 358 ASN B 373 1 16 HELIX 37 37 ASN B 403 PHE B 409 1 7 HELIX 38 38 HIS B 421 LEU B 426 5 6 HELIX 39 39 GLY B 450 ARG B 468 1 19 HELIX 40 40 PHE B 473 LEU B 477 5 5 SHEET 1 A 4 ILE A 76 LEU A 81 0 SHEET 2 A 4 ILE A 84 ASN A 90 -1 O VAL A 88 N PHE A 77 SHEET 3 A 4 THR A 399 ASN A 403 1 O ILE A 401 N LEU A 89 SHEET 4 A 4 HIS A 381 ALA A 382 -1 N HIS A 381 O VAL A 400 SHEET 1 B 2 ALA A 387 VAL A 389 0 SHEET 2 B 2 TYR A 392 ILE A 394 -1 O ILE A 394 N ALA A 387 SHEET 1 C 2 PHE A 469 HIS A 472 0 SHEET 2 C 2 CYS A 497 ARG A 500 -1 O CYS A 497 N HIS A 472 SHEET 1 D 4 ILE B 76 LEU B 81 0 SHEET 2 D 4 ILE B 84 LEU B 89 -1 O VAL B 88 N PHE B 77 SHEET 3 D 4 THR B 399 THR B 402 1 O THR B 399 N VAL B 87 SHEET 4 D 4 HIS B 381 ALA B 382 -1 N HIS B 381 O VAL B 400 SHEET 1 E 2 ALA B 387 VAL B 389 0 SHEET 2 E 2 TYR B 392 ILE B 394 -1 O ILE B 394 N ALA B 387 SHEET 1 F 2 PHE B 469 HIS B 472 0 SHEET 2 F 2 CYS B 497 ARG B 500 -1 O GLU B 499 N HIS B 470 LINK O4 GLC C 1 C1 GLC C 2 1555 1555 1.43 LINK C1 GLC C 1 O4 GLC C 7 1555 1555 1.42 LINK O4 GLC C 2 C1 GLC C 3 1555 1555 1.45 LINK O4 GLC C 3 C1 GLC C 4 1555 1555 1.44 LINK O4 GLC C 4 C1 GLC C 5 1555 1555 1.43 LINK O4 GLC C 5 C1 GLC C 6 1555 1555 1.45 LINK O4 GLC C 6 C1 GLC C 7 1555 1555 1.44 LINK O4 GLC D 1 C1 GLC D 2 1555 1555 1.42 LINK C1 GLC D 1 O4 GLC D 7 1555 1555 1.45 LINK O4 GLC D 2 C1 GLC D 3 1555 1555 1.43 LINK O4 GLC D 3 C1 GLC D 4 1555 1555 1.45 LINK O4 GLC D 4 C1 GLC D 5 1555 1555 1.43 LINK O4 GLC D 5 C1 GLC D 6 1555 1555 1.43 LINK O4 GLC D 6 C1 GLC D 7 1555 1555 1.41 LINK SG CYS A 448 FE AHEM A 601 1555 1555 2.48 LINK SG CYS A 448 FE BHEM A 601 1555 1555 1.95 LINK SG CYS B 448 FE AHEM B 601 1555 1555 2.19 CRYST1 137.303 163.040 152.588 90.00 90.00 90.00 C 2 2 21 16 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 0.007283 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006133 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006554 0.00000