HEADER TRANSCRIPTION 03-JUN-17 5XPN
TITLE CRYSTAL STRUCTURE OF VDR-LBD COMPLEXED WITH 25RS-(HYDROXYPHENYL)-25-
TITLE 2 METHOXY-2-METHYLIDENE-19,26,27-TRINOR-1-HYDROXYVITAMIN D3
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 116-423;
COMPND 5 SYNONYM: VDR,1,25-DIHYDROXYVITAMIN D3 RECEPTOR,NUCLEAR RECEPTOR
COMPND 6 SUBFAMILY 1 GROUP I MEMBER 1;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 1;
COMPND 11 CHAIN: C;
COMPND 12 FRAGMENT: UNP RESIDUES 640-652;
COMPND 13 SYNONYM: ACTIVATOR-RECRUITED COFACTOR 205 KDA COMPONENT,ARC205,
COMPND 14 MEDIATOR COMPLEX SUBUNIT 1,PEROXISOME PROLIFERATOR-ACTIVATED
COMPND 15 RECEPTOR-BINDING PROTEIN,PPAR-BINDING PROTEIN,THYROID HORMONE
COMPND 16 RECEPTOR-ASSOCIATED PROTEIN COMPLEX 220 KDA COMPONENT,TRAP220,THYROID
COMPND 17 RECEPTOR-INTERACTING PROTEIN 2,TRIP-2,VITAMIN D RECEPTOR-INTERACTING
COMPND 18 PROTEIN COMPLEX COMPONENT DRIP205,P53 REGULATORY PROTEIN RB18A;
COMPND 19 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE 3 ORGANISM_COMMON: RAT;
SOURCE 4 ORGANISM_TAXID: 10116;
SOURCE 5 GENE: VDR, NR1I1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 10 ORGANISM_COMMON: HUMAN;
SOURCE 11 ORGANISM_TAXID: 9606;
SOURCE 12 GENE: MED1, ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP,
SOURCE 13 PPARGBP, RB18A, TRAP220, TRIP2;
SOURCE 14 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT;
SOURCE 15 EXPRESSION_SYSTEM_TAXID: 32630
KEYWDS TRANSCRIPTION, VITAMIN D3, VDR, VDRE, RXR, CO-FACTORS
EXPDTA X-RAY DIFFRACTION
AUTHOR A.KATO,T.ITOH,K.YAMAMOTO
REVDAT 2 27-MAR-24 5XPN 1 REMARK
REVDAT 1 11-JUL-18 5XPN 0
JRNL AUTH A.KATO,M.YAMAO,Y.HASHIHARA,H.ISHIDA,T.ITOH,K.YAMAMOTO
JRNL TITL VITAMIN D ANALOGUES WITH A P-HYDROXYPHENYL GROUP AT THE C25
JRNL TITL 2 POSITION: CRYSTAL STRUCTURE OF VITAMIN D RECEPTOR
JRNL TITL 3 LIGAND-BINDING DOMAIN COMPLEXED WITH THE LIGAND EXPLAINS THE
JRNL TITL 4 MECHANISM UNDERLYING FULL ANTAGONISTIC ACTION
JRNL REF J. MED. CHEM. V. 60 8394 2017
JRNL REFN ISSN 1520-4804
JRNL PMID 28954197
JRNL DOI 10.1021/ACS.JMEDCHEM.7B00819
REMARK 2
REMARK 2 RESOLUTION. 1.96 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0049
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.95
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9
REMARK 3 NUMBER OF REFLECTIONS : 17130
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) : 0.210
REMARK 3 R VALUE (WORKING SET) : 0.207
REMARK 3 FREE R VALUE : 0.256
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 919
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) : 1.96
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1387
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.91
REMARK 3 BIN R VALUE (WORKING SET) : 0.2730
REMARK 3 BIN FREE R VALUE SET COUNT : 61
REMARK 3 BIN FREE R VALUE : 0.3080
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2001
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 72
REMARK 3 SOLVENT ATOMS : 158
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.33
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -3.08000
REMARK 3 B22 (A**2) : 3.62000
REMARK 3 B33 (A**2) : -0.34000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -1.05000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.223
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.191
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.166
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.347
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2119 ; 0.015 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 2091 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2869 ; 1.872 ; 2.023
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4834 ; 0.884 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 247 ; 5.598 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;37.889 ;24.556
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 385 ;17.658 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;23.971 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 328 ; 0.091 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2282 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 455 ; 0.004 ; 0.020
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): 997 ; 2.863 ; 3.286
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 996 ; 2.863 ; 3.284
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1241 ; 4.237 ; 4.902
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1242 ; 4.236 ; 4.904
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1122 ; 3.482 ; 3.655
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1123 ; 3.480 ; 3.654
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1629 ; 5.303 ; 5.314
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2552 ; 7.295 ;27.101
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2530 ; 7.303 ;26.951
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 : NULL
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: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 5XPN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUN-17.
REMARK 100 THE DEPOSITION ID IS D_1300003893.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-JUN-16
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 : PHOTON FACTORY
REMARK 200 BEAMLINE : AR-NE3A
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 : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18216
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960
REMARK 200 RESOLUTION RANGE LOW (A) : 32.950
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 91.9
REMARK 200 DATA REDUNDANCY : 2.900
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.01
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: MOPS-NA, NA-FORMATE, PEG 4000,
REMARK 280 ETHYLENEGLYCOL, PH 7.0, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -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 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 76.87000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.58000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 76.87000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.58000
REMARK 290 SMTRY3 4 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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1130 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11590 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL
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 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 GLY A 106
REMARK 465 SER A 107
REMARK 465 HIS A 108
REMARK 465 MET A 109
REMARK 465 GLY A 110
REMARK 465 SER A 111
REMARK 465 PRO A 112
REMARK 465 ASN A 113
REMARK 465 SER A 114
REMARK 465 PRO A 115
REMARK 465 LEU A 116
REMARK 465 LYS A 117
REMARK 465 ASP A 118
REMARK 465 SER A 119
REMARK 465 LEU A 120
REMARK 465 ARG A 121
REMARK 465 PRO A 122
REMARK 465 ASP A 207
REMARK 465 GLY A 208
REMARK 465 SER A 209
REMARK 465 THR A 210
REMARK 465 GLY A 211
REMARK 465 SER A 212
REMARK 465 VAL A 213
REMARK 465 THR A 214
REMARK 465 LEU A 215
REMARK 465 ASP A 216
REMARK 465 LEU A 217
REMARK 465 ASN A 420
REMARK 465 GLU A 421
REMARK 465 ILE A 422
REMARK 465 SER A 423
REMARK 465 ASP C 636
REMARK 465 ASN C 637
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 PHE A 402 CG CD1 CD2 CE1 CE2 CZ
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 OG1 THR A 294 O HOH A 601 2.18
REMARK 500 OD1 ASP A 295 O HOH A 602 2.18
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 ASP A 292 CB - CG - OD2 ANGL. DEV. = 5.5 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 CYS A 284 34.02 -94.87
REMARK 500 GLN A 343 -71.92 -85.21
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 THE TWO ISOMERS 8BO AND 9RO DIFFER IN CONFIGURATION AT C27. 8BO HAS
REMARK 600 S CONFIGURATION AT C27, BUT 9RO HAS R CONFIGURATION AT C27.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8BO A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 9RO A 502
DBREF 5XPN A 116 423 UNP P13053 VDR_RAT 116 423
DBREF 5XPN C 625 637 PDB 5XPN 5XPN 625 637
SEQADV 5XPN GLY A 106 UNP P13053 EXPRESSION TAG
SEQADV 5XPN SER A 107 UNP P13053 EXPRESSION TAG
SEQADV 5XPN HIS A 108 UNP P13053 EXPRESSION TAG
SEQADV 5XPN MET A 109 UNP P13053 EXPRESSION TAG
SEQADV 5XPN GLY A 110 UNP P13053 EXPRESSION TAG
SEQADV 5XPN SER A 111 UNP P13053 EXPRESSION TAG
SEQADV 5XPN PRO A 112 UNP P13053 EXPRESSION TAG
SEQADV 5XPN ASN A 113 UNP P13053 EXPRESSION TAG
SEQADV 5XPN SER A 114 UNP P13053 EXPRESSION TAG
SEQADV 5XPN PRO A 115 UNP P13053 EXPRESSION TAG
SEQADV 5XPN A UNP P13053 SER 165 DELETION
SEQADV 5XPN A UNP P13053 TYR 166 DELETION
SEQADV 5XPN A UNP P13053 SER 167 DELETION
SEQADV 5XPN A UNP P13053 PRO 168 DELETION
SEQADV 5XPN A UNP P13053 ARG 169 DELETION
SEQADV 5XPN A UNP P13053 PRO 170 DELETION
SEQADV 5XPN A UNP P13053 THR 171 DELETION
SEQADV 5XPN A UNP P13053 LEU 172 DELETION
SEQADV 5XPN A UNP P13053 SER 173 DELETION
SEQADV 5XPN A UNP P13053 PHE 174 DELETION
SEQADV 5XPN A UNP P13053 SER 175 DELETION
SEQADV 5XPN A UNP P13053 GLY 176 DELETION
SEQADV 5XPN A UNP P13053 ASN 177 DELETION
SEQADV 5XPN A UNP P13053 SER 178 DELETION
SEQADV 5XPN A UNP P13053 SER 179 DELETION
SEQADV 5XPN A UNP P13053 SER 180 DELETION
SEQADV 5XPN A UNP P13053 SER 181 DELETION
SEQADV 5XPN A UNP P13053 SER 182 DELETION
SEQADV 5XPN A UNP P13053 SER 183 DELETION
SEQADV 5XPN A UNP P13053 ASP 184 DELETION
SEQADV 5XPN A UNP P13053 LEU 185 DELETION
SEQADV 5XPN A UNP P13053 TYR 186 DELETION
SEQADV 5XPN A UNP P13053 THR 187 DELETION
SEQADV 5XPN A UNP P13053 THR 188 DELETION
SEQADV 5XPN A UNP P13053 SER 189 DELETION
SEQADV 5XPN A UNP P13053 LEU 190 DELETION
SEQADV 5XPN A UNP P13053 ASP 191 DELETION
SEQADV 5XPN A UNP P13053 MET 192 DELETION
SEQADV 5XPN A UNP P13053 MET 193 DELETION
SEQADV 5XPN A UNP P13053 GLU 194 DELETION
SEQADV 5XPN A UNP P13053 PRO 195 DELETION
SEQADV 5XPN A UNP P13053 SER 196 DELETION
SEQADV 5XPN A UNP P13053 GLY 197 DELETION
SEQADV 5XPN A UNP P13053 PHE 198 DELETION
SEQADV 5XPN A UNP P13053 SER 199 DELETION
SEQADV 5XPN A UNP P13053 ASN 200 DELETION
SEQADV 5XPN A UNP P13053 LEU 201 DELETION
SEQADV 5XPN A UNP P13053 ASP 202 DELETION
SEQADV 5XPN A UNP P13053 LEU 203 DELETION
SEQADV 5XPN A UNP P13053 ASN 204 DELETION
SEQADV 5XPN A UNP P13053 GLY 205 DELETION
SEQADV 5XPN A UNP P13053 GLU 206 DELETION
SEQADV 5XPN A UNP P13053 ASP 207 DELETION
SEQADV 5XPN A UNP P13053 SER 208 DELETION
SEQADV 5XPN A UNP P13053 ASP 209 DELETION
SEQADV 5XPN A UNP P13053 ASP 210 DELETION
SEQADV 5XPN A UNP P13053 PRO 211 DELETION
SEQRES 1 A 271 GLY SER HIS MET GLY SER PRO ASN SER PRO LEU LYS ASP
SEQRES 2 A 271 SER LEU ARG PRO LYS LEU SER GLU GLU GLN GLN HIS ILE
SEQRES 3 A 271 ILE ALA ILE LEU LEU ASP ALA HIS HIS LYS THR TYR ASP
SEQRES 4 A 271 PRO THR TYR ALA ASP PHE ARG ASP PHE ARG PRO PRO VAL
SEQRES 5 A 271 ARG MET ASP GLY SER THR GLY SER VAL THR LEU ASP LEU
SEQRES 6 A 271 SER PRO LEU SER MET LEU PRO HIS LEU ALA ASP LEU VAL
SEQRES 7 A 271 SER TYR SER ILE GLN LYS VAL ILE GLY PHE ALA LYS MET
SEQRES 8 A 271 ILE PRO GLY PHE ARG ASP LEU THR SER ASP ASP GLN ILE
SEQRES 9 A 271 VAL LEU LEU LYS SER SER ALA ILE GLU VAL ILE MET LEU
SEQRES 10 A 271 ARG SER ASN GLN SER PHE THR MET ASP ASP MET SER TRP
SEQRES 11 A 271 ASP CYS GLY SER GLN ASP TYR LYS TYR ASP VAL THR ASP
SEQRES 12 A 271 VAL SER LYS ALA GLY HIS THR LEU GLU LEU ILE GLU PRO
SEQRES 13 A 271 LEU ILE LYS PHE GLN VAL GLY LEU LYS LYS LEU ASN LEU
SEQRES 14 A 271 HIS GLU GLU GLU HIS VAL LEU LEU MET ALA ILE CYS ILE
SEQRES 15 A 271 VAL SER PRO ASP ARG PRO GLY VAL GLN ASP ALA LYS LEU
SEQRES 16 A 271 VAL GLU ALA ILE GLN ASP ARG LEU SER ASN THR LEU GLN
SEQRES 17 A 271 THR TYR ILE ARG CYS ARG HIS PRO PRO PRO GLY SER HIS
SEQRES 18 A 271 GLN LEU TYR ALA LYS MET ILE GLN LYS LEU ALA ASP LEU
SEQRES 19 A 271 ARG SER LEU ASN GLU GLU HIS SER LYS GLN TYR ARG SER
SEQRES 20 A 271 LEU SER PHE GLN PRO GLU ASN SER MET LYS LEU THR PRO
SEQRES 21 A 271 LEU VAL LEU GLU VAL PHE GLY ASN GLU ILE SER
SEQRES 1 C 13 LYS ASN HIS PRO MET LEU MET ASN LEU LEU LYS ASP ASN
HET 8BO A 501 36
HET 9RO A 502 36
HETNAM 8BO (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{A}~{S},
HETNAM 2 8BO 7~{A}~{R})-1-[(2~{R},6~{S})-6-(4-HYDROXYPHENYL)-6-
HETNAM 3 8BO METHOXY-HEXAN-2-YL]-7~{A}-METHYL-2,3,3~{A},5,6,7-
HETNAM 4 8BO HEXAHYDRO-1~{H}-INDEN-4-YLIDENE]ETHYLIDENE]-2-
HETNAM 5 8BO METHYLIDENE-CYCLOHEXANE-1,3-DIOL
HETNAM 9RO (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{A}~{S},
HETNAM 2 9RO 7~{A}~{R})-1-[(2~{R},6~{R})-6-(4-HYDROXYPHENYL)-6-
HETNAM 3 9RO METHOXY-HEXAN-2-YL]-7~{A}-METHYL-2,3,3~{A},5,6,7-
HETNAM 4 9RO HEXAHYDRO-1~{H}-INDEN-4-YLIDENE]ETHYLIDENE]-2-
HETNAM 5 9RO METHYLIDENE-CYCLOHEXANE-1,3-DIOL
HETSYN 8BO 25RS-(HYDROXYPHENYL)-25-METHOXY-2-METHYLIDENE-19,26,27-
HETSYN 2 8BO TRINOR-1-HYDROXYVITAMIN D3
FORMUL 3 8BO C32 H46 O4
FORMUL 4 9RO C32 H46 O4
FORMUL 5 HOH *158(H2 O)
HELIX 1 AA1 SER A 125 TYR A 143 1 19
HELIX 2 AA2 TYR A 147 PHE A 153 5 7
HELIX 3 AA3 MET A 222 MET A 243 1 22
HELIX 4 AA4 GLY A 246 LEU A 250 5 5
HELIX 5 AA5 THR A 251 ASN A 272 1 22
HELIX 6 AA6 SER A 286 ASP A 288 5 3
HELIX 7 AA7 ASP A 292 LYS A 298 1 7
HELIX 8 AA8 THR A 302 LYS A 318 1 17
HELIX 9 AA9 HIS A 322 VAL A 335 1 14
HELIX 10 AB1 ASP A 344 HIS A 367 1 24
HELIX 11 AB2 GLN A 374 PHE A 402 1 29
HELIX 12 AB3 GLN A 403 MET A 408 1 6
HELIX 13 AB4 THR A 411 GLY A 419 1 9
HELIX 14 AB5 HIS C 627 LYS C 635 1 9
SHEET 1 AA1 3 PHE A 275 THR A 276 0
SHEET 2 AA1 3 SER A 281 ASP A 283 -1 O SER A 281 N THR A 276
SHEET 3 AA1 3 LYS A 290 TYR A 291 -1 O TYR A 291 N TRP A 282
CISPEP 1 PRO A 369 PRO A 370 0 1.69
SITE 1 AC1 17 TYR A 143 LEU A 223 VAL A 230 SER A 233
SITE 2 AC1 17 ARG A 270 SER A 271 SER A 274 TRP A 282
SITE 3 AC1 17 CYS A 284 VAL A 296 ALA A 299 GLY A 300
SITE 4 AC1 17 HIS A 301 HIS A 393 GLN A 396 LEU A 400
SITE 5 AC1 17 9RO A 502
SITE 1 AC2 17 TYR A 143 LEU A 223 VAL A 230 SER A 233
SITE 2 AC2 17 ARG A 270 SER A 271 SER A 274 TRP A 282
SITE 3 AC2 17 CYS A 284 VAL A 296 ALA A 299 GLY A 300
SITE 4 AC2 17 HIS A 301 HIS A 393 GLN A 396 LEU A 400
SITE 5 AC2 17 8BO A 501
CRYST1 153.740 43.160 42.030 90.00 95.32 90.00 C 1 2 1 4
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 0.006504 0.000000 0.000606 0.00000
SCALE2 0.000000 0.023170 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023895 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
