HEADER GENE REGULATION 02-NOV-99 1DB1
TITLE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED TO
TITLE 2 VITAMIN D
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: VITAMIN D NUCLEAR RECEPTOR;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN;
COMPND 5 SYNONYM: VDR;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS COMPLEX, GENE REGULATION
EXPDTA X-RAY DIFFRACTION
AUTHOR N.ROCHEL,J.M.WURTZ,A.MITSCHLER,B.KLAHOLZ,D.MORAS
REVDAT 4 07-FEB-24 1DB1 1 REMARK
REVDAT 3 16-AUG-17 1DB1 1 SOURCE REMARK
REVDAT 2 24-FEB-09 1DB1 1 VERSN
REVDAT 1 31-JAN-00 1DB1 0
JRNL AUTH N.ROCHEL,J.M.WURTZ,A.MITSCHLER,B.KLAHOLZ,D.MORAS
JRNL TITL THE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D
JRNL TITL 2 BOUND TO ITS NATURAL LIGAND.
JRNL REF MOL.CELL V. 5 173 2000
JRNL REFN ISSN 1097-2765
JRNL PMID 10678179
JRNL DOI 10.1016/S1097-2765(00)80413-X
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.6
REMARK 3 NUMBER OF REFLECTIONS : 28808
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.191
REMARK 3 FREE R VALUE : 0.214
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 2879
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 : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
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 : 1992
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 30
REMARK 3 SOLVENT ATOMS : 164
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 26.00
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : NULL
REMARK 3 BOND ANGLES (DEGREES) : NULL
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1DB1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-99.
REMARK 100 THE DEPOSITION ID IS D_1000009937.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-JUL-98
REMARK 200 TEMPERATURE (KELVIN) : 298.0
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 4
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG
REMARK 200 BEAMLINE : BW7B
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.8345
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29434
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4
REMARK 200 DATA REDUNDANCY : 4.100
REMARK 200 R MERGE (I) : 0.06100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3
REMARK 200 DATA REDUNDANCY IN SHELL : 2.80
REMARK 200 R MERGE FOR SHELL (I) : 0.24000
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: NULL
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.20
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MES, PH 6.0, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K
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 22.59650
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.64300
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.22150
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.64300
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.59650
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.22150
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 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 ASP A 118
REMARK 465 SER A 119
REMARK 465 GLY A 375
REMARK 465 SER A 376
REMARK 465 HIS A 377
REMARK 465 ASN A 424
REMARK 465 GLU A 425
REMARK 465 ILE A 426
REMARK 465 SER A 427
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 LEU A 378 C LEU A 379 N 0.225
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 ASP A 161 49.86 -154.99
REMARK 500 CYS A 288 51.04 -114.77
REMARK 500 ASP A 342 40.92 -97.01
REMARK 500 LEU A 414 -156.16 -106.91
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 VDX A 428
DBREF 1DB1 A 118 164 UNP P11473 VDR_HUMAN 118 164
DBREF 1DB1 A 216 427 UNP P11473 VDR_HUMAN 216 427
SEQRES 1 A 259 ASP SER LEU ARG PRO LYS LEU SER GLU GLU GLN GLN ARG
SEQRES 2 A 259 ILE ILE ALA ILE LEU LEU ASP ALA HIS HIS LYS THR TYR
SEQRES 3 A 259 ASP PRO THR TYR SER ASP PHE CYS GLN PHE ARG PRO PRO
SEQRES 4 A 259 VAL ARG VAL ASN ASP GLY GLY GLY SER VAL THR LEU GLU
SEQRES 5 A 259 LEU SER GLN LEU SER MET LEU PRO HIS LEU ALA ASP LEU
SEQRES 6 A 259 VAL SER TYR SER ILE GLN LYS VAL ILE GLY PHE ALA LYS
SEQRES 7 A 259 MET ILE PRO GLY PHE ARG ASP LEU THR SER GLU ASP GLN
SEQRES 8 A 259 ILE VAL LEU LEU LYS SER SER ALA ILE GLU VAL ILE MET
SEQRES 9 A 259 LEU ARG SER ASN GLU SER PHE THR MET ASP ASP MET SER
SEQRES 10 A 259 TRP THR CYS GLY ASN GLN ASP TYR LYS TYR ARG VAL SER
SEQRES 11 A 259 ASP VAL THR LYS ALA GLY HIS SER LEU GLU LEU ILE GLU
SEQRES 12 A 259 PRO LEU ILE LYS PHE GLN VAL GLY LEU LYS LYS LEU ASN
SEQRES 13 A 259 LEU HIS GLU GLU GLU HIS VAL LEU LEU MET ALA ILE CYS
SEQRES 14 A 259 ILE VAL SER PRO ASP ARG PRO GLY VAL GLN ASP ALA ALA
SEQRES 15 A 259 LEU ILE GLU ALA ILE GLN ASP ARG LEU SER ASN THR LEU
SEQRES 16 A 259 GLN THR TYR ILE ARG CYS ARG HIS PRO PRO PRO GLY SER
SEQRES 17 A 259 HIS LEU LEU TYR ALA LYS MET ILE GLN LYS LEU ALA ASP
SEQRES 18 A 259 LEU ARG SER LEU ASN GLU GLU HIS SER LYS GLN TYR ARG
SEQRES 19 A 259 CYS LEU SER PHE GLN PRO GLU CYS SER MET LYS LEU THR
SEQRES 20 A 259 PRO LEU VAL LEU GLU VAL PHE GLY ASN GLU ILE SER
HET VDX A 428 30
HETNAM VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-
HETNAM 2 VDX OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-
HETNAM 3 VDX CYCLOHEXANE-1,3-DIOL
HETSYN VDX 1,25 DIHYDROXY VITAMIN D3
FORMUL 2 VDX C27 H44 O3
FORMUL 3 HOH *164(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 LEU A 323 1 18
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 378 PHE A 406 1 29
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 N TYR A 295 O TRP A 286
CISPEP 1 PRO A 373 PRO A 374 0 -0.13
SITE 1 AC1 12 TYR A 143 LEU A 227 LEU A 233 VAL A 234
SITE 2 AC1 12 SER A 237 ARG A 274 SER A 275 SER A 278
SITE 3 AC1 12 TRP A 286 CYS A 288 HIS A 305 HIS A 397
CRYST1 45.193 52.443 133.286 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 0.022127 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019068 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007503 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
