HEADER GENE REGULATION 09-APR-01 1IE8
TITLE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D LIGAND BINDING
TITLE 2 DOMAIN BOUND TO KH1060
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: 1,25-DIHYDROXYVITAMIN D3 RECEPTOR;
COMPND 5 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
KEYWDS VDR, KH1060, GENE REGULATION
EXPDTA X-RAY DIFFRACTION
AUTHOR G.TOCCHINI-VALENTINI,N.ROCHEL,J.M.WURTZ,A.MITSCHLER,D.MORAS
REVDAT 4 07-FEB-24 1IE8 1 REMARK
REVDAT 3 16-AUG-17 1IE8 1 SOURCE REMARK
REVDAT 2 24-FEB-09 1IE8 1 VERSN
REVDAT 1 16-MAY-01 1IE8 0
JRNL AUTH G.TOCCHINI-VALENTINI,N.ROCHEL,J.M.WURTZ,A.MITSCHLER,D.MORAS
JRNL TITL CRYSTAL STRUCTURES OF THE VITAMIN D RECEPTOR COMPLEXED TO
JRNL TITL 2 SUPERAGONIST 20-EPI LIGANDS.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 98 5491 2001
JRNL REFN ISSN 0027-8424
JRNL PMID 11344298
JRNL DOI 10.1073/PNAS.091018698
REMARK 2
REMARK 2 RESOLUTION. 1.52 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) : 1.52
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 45925
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 SET) : 0.212
REMARK 3 FREE R VALUE : 0.230
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 4678
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 : 33
REMARK 3 SOLVENT ATOMS : 214
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
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) : 0.011
REMARK 3 BOND ANGLES (DEGREES) : 1.500
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 1IE8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-01.
REMARK 100 THE DEPOSITION ID IS D_1000013200.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : BM30A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
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 : CCP4 (TRUNCATE)
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45925
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1
REMARK 200 DATA REDUNDANCY : 4.800
REMARK 200 R MERGE (I) : 0.04800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.29000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
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 (%): 52.28
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 6.0, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, 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 22.24500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.69500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.93500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.69500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.24500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.93500
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: 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 45.83 -153.56
REMARK 500 ASP A 283 15.86 -141.59
REMARK 500 ARG A 368 40.97 -85.76
REMARK 500 CYS A 369 -46.29 -154.46
REMARK 500 LEU A 414 -154.43 -99.40
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 KH1 A 500
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1DB1 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED
REMARK 900 TO VITAMIN D
REMARK 900 RELATED ID: 1IE9 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D LIGAND
REMARK 900 BINDING DOMAIN BOUND TO MC1288
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE PROTEIN HAS BEEN GENETICALLY ENGINEERED TO
REMARK 999 LACK RESIDUES 165-215.
DBREF 1IE8 A 118 164 UNP P11473 VDR_HUMAN 118 164
DBREF 1IE8 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 KH1 A 500 33
HETNAM KH1 5-(2-{1-[1-(4-ETHYL-4-HYDROXY-HEXYLOXY)-ETHYL]-7A-
HETNAM 2 KH1 METHYL-OCTAHYDRO-INDEN-4-YLIDENE}-ETHYLIDENE)-4-
HETNAM 3 KH1 METHYLENE-CYCLOHEXANE-1,3-DIOL
HETSYN KH1 1ALPHA,25-DIHYDROXYL-20-EPI-22-OXA-24,26,27-TRIHOMO
HETSYN 2 KH1 VITAMIN D3
FORMUL 2 KH1 C29 H48 O4
FORMUL 3 HOH *214(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 GLU A 409 LEU A 414 5 6
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 -0.09
SITE 1 AC1 13 TYR A 143 LEU A 227 VAL A 234 SER A 237
SITE 2 AC1 13 ARG A 274 SER A 275 SER A 278 TRP A 286
SITE 3 AC1 13 CYS A 288 ALA A 303 HIS A 305 HIS A 397
SITE 4 AC1 13 LEU A 404
CRYST1 44.490 51.870 131.390 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 0.022477 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019279 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007611 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
