HEADER HORMONE RECEPTOR 05-NOV-12 3W0Y
TITLE CRYSTAL STRUCTURE ANALYSIS OF VITAMIN D RECEPTOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 120-164, 216-423;
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 OTHER_DETAILS: FUSION PROTEIN OF RESIDUES 120-164 AND RESIDUES 216-
COMPND 9 423
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: VDR, NR1I1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS VITAMIN D RECEPTOR, HORMONE RECEPTOR
EXPDTA X-RAY DIFFRACTION
AUTHOR S.ITOH,S.IIJIMA
REVDAT 3 20-MAR-24 3W0Y 1 REMARK
REVDAT 2 16-AUG-17 3W0Y 1 SOURCE REMARK
REVDAT 1 13-NOV-13 3W0Y 0
JRNL AUTH H.KASHIWAGI,Y.ONO,S.ITOH,S.IIJIMA,F.ICHIKAWA,S.HARADA,
JRNL AUTH 2 S.TAKEDA,N.SEKIGUCHI,M.ISHIGAI,T.TAKAHASHI
JRNL TITL CRYSTAL STRUCTURE ANALYSIS OF VITAMIN D RECEPTOR
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.98 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER-TNT BUSTER 2.11.2
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.87
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8
REMARK 3 NUMBER OF REFLECTIONS : 20132
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) : 0.177
REMARK 3 R VALUE (WORKING SET) : 0.175
REMARK 3 FREE R VALUE : 0.218
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070
REMARK 3 FREE R VALUE TEST SET COUNT : 1021
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 : 10
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.09
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.83
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2878
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1867
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2727
REMARK 3 BIN R VALUE (WORKING SET) : 0.1833
REMARK 3 BIN FREE R VALUE : 0.2464
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.25
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 151
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 : 1993
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 42
REMARK 3 SOLVENT ATOMS : 281
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 27.57
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.73
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.50860
REMARK 3 B22 (A**2) : -0.42280
REMARK 3 B33 (A**2) : -1.08580
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 COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.188
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.186
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.159
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.164
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.151
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 2078 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 2817 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 729 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 53 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 289 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 2078 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 268 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 2724 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 0.98
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.63
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.28
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3W0Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-OCT-13.
REMARK 100 THE DEPOSITION ID IS D_1000095747.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-OCT-05
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.3
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL32B2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : SILICONE
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22329
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910
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 (%) : 90.4
REMARK 200 DATA REDUNDANCY : 3.800
REMARK 200 R MERGE (I) : 0.08800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98
REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9
REMARK 200 DATA REDUNDANCY IN SHELL : 3.60
REMARK 200 R MERGE FOR SHELL (I) : 0.55500
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: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.88
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.3, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 22.60850
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.33200
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.56200
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.33200
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.60850
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.56200
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: 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 GLY A 375
REMARK 465 SER A 376
REMARK 465 HIS A 377
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 ASP A 161 58.58 -148.01
REMARK 500 ASP A 283 15.60 -144.45
REMARK 500 ASN A 290 -177.41 -65.77
REMARK 500 TYR A 293 41.49 -104.99
REMARK 500 ASP A 342 34.99 -88.67
REMARK 500 LEU A 414 -156.65 -97.33
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DS4 A 501
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3W0A RELATED DB: PDB
REMARK 900 RELATED ID: 3W0C RELATED DB: PDB
DBREF 3W0Y A 120 164 UNP P11473 VDR_HUMAN 120 164
DBREF 3W0Y A 216 423 UNP P11473 VDR_HUMAN 216 423
SEQRES 1 A 253 LEU ARG PRO LYS LEU SER GLU GLU GLN GLN ARG ILE ILE
SEQRES 2 A 253 ALA ILE LEU LEU ASP ALA HIS HIS LYS THR TYR ASP PRO
SEQRES 3 A 253 THR TYR SER ASP PHE CYS GLN PHE ARG PRO PRO VAL ARG
SEQRES 4 A 253 VAL ASN ASP GLY GLY GLY SER VAL THR LEU GLU LEU SER
SEQRES 5 A 253 GLN LEU SER MET LEU PRO HIS LEU ALA ASP LEU VAL SER
SEQRES 6 A 253 TYR SER ILE GLN LYS VAL ILE GLY PHE ALA LYS MET ILE
SEQRES 7 A 253 PRO GLY PHE ARG ASP LEU THR SER GLU ASP GLN ILE VAL
SEQRES 8 A 253 LEU LEU LYS SER SER ALA ILE GLU VAL ILE MET LEU ARG
SEQRES 9 A 253 SER ASN GLU SER PHE THR MET ASP ASP MET SER TRP THR
SEQRES 10 A 253 CYS GLY ASN GLN ASP TYR LYS TYR ARG VAL SER ASP VAL
SEQRES 11 A 253 THR LYS ALA GLY HIS SER LEU GLU LEU ILE GLU PRO LEU
SEQRES 12 A 253 ILE LYS PHE GLN VAL GLY LEU LYS LYS LEU ASN LEU HIS
SEQRES 13 A 253 GLU GLU GLU HIS VAL LEU LEU MET ALA ILE CYS ILE VAL
SEQRES 14 A 253 SER PRO ASP ARG PRO GLY VAL GLN ASP ALA ALA LEU ILE
SEQRES 15 A 253 GLU ALA ILE GLN ASP ARG LEU SER ASN THR LEU GLN THR
SEQRES 16 A 253 TYR ILE ARG CYS ARG HIS PRO PRO PRO GLY SER HIS LEU
SEQRES 17 A 253 LEU TYR ALA LYS MET ILE GLN LYS LEU ALA ASP LEU ARG
SEQRES 18 A 253 SER LEU ASN GLU GLU HIS SER LYS GLN TYR ARG CYS LEU
SEQRES 19 A 253 SER PHE GLN PRO GLU CYS SER MET LYS LEU THR PRO LEU
SEQRES 20 A 253 VAL LEU GLU VAL PHE GLY
HET DS4 A 501 42
HETNAM DS4 [3-FLUORO-2'-METHYL-4'-(3-{3-METHYL-4-[(1E)-4,4,4-
HETNAM 2 DS4 TRIFLUORO-3-HYDROXY-3-(TRIFLUOROMETHYL)BUT-1-EN-1-
HETNAM 3 DS4 YL]PHENYL}PENTAN-3-YL)BIPHENYL-4-YL]ACETIC ACID
FORMUL 2 DS4 C32 H31 F7 O3
FORMUL 3 HOH *281(H2 O)
HELIX 1 1 SER A 125 TYR A 143 1 19
HELIX 2 2 ASP A 149 PHE A 153 5 5
HELIX 3 3 SER A 216 LEU A 224 1 9
HELIX 4 4 MET A 226 MET A 247 1 22
HELIX 5 5 GLY A 250 LEU A 254 5 5
HELIX 6 6 THR A 255 SER A 275 1 21
HELIX 7 7 ASN A 290 ASP A 292 5 3
HELIX 8 8 ARG A 296 LYS A 302 1 7
HELIX 9 9 SER A 306 LYS A 322 1 17
HELIX 10 10 HIS A 326 VAL A 339 1 14
HELIX 11 11 ASP A 348 HIS A 371 1 24
HELIX 12 12 LEU A 379 PHE A 406 1 28
HELIX 13 13 CYS A 410 LEU A 414 5 5
HELIX 14 14 THR A 415 GLY A 423 1 9
SHEET 1 A 3 PHE A 279 THR A 280 0
SHEET 2 A 3 SER A 285 THR A 287 -1 O SER A 285 N THR A 280
SHEET 3 A 3 LYS A 294 TYR A 295 -1 O TYR A 295 N TRP A 286
CISPEP 1 PRO A 373 PRO A 374 0 -1.94
SITE 1 AC1 22 TYR A 143 ASP A 144 PHE A 150 LEU A 227
SITE 2 AC1 22 ALA A 231 VAL A 234 TYR A 236 SER A 237
SITE 3 AC1 22 ILE A 268 ARG A 274 SER A 275 TRP A 286
SITE 4 AC1 22 CYS A 288 HIS A 305 HIS A 397 TYR A 401
SITE 5 AC1 22 LEU A 404 LEU A 414 VAL A 418 PHE A 422
SITE 6 AC1 22 HOH A 608 HOH A 617
CRYST1 45.217 51.124 132.664 90.00 90.00 90.00 P 21 21 21 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 0.022116 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019560 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007538 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
