PDB Short entry for 3W0C HEADER HORMONE RECEPTOR 29-OCT-12 3W0C 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 3W0C 1 REMARK REVDAT 2 16-AUG-17 3W0C 1 SOURCE REMARK REVDAT 1 13-NOV-13 3W0C 0 JRNL AUTH H.KASHIWAGI,M.OHTA,Y.ONO,S.ITOH,S.IIJIMA,H.SATO,T.TAKAHASHI JRNL TITL STRUCTURE ANALYSIS OF VITAMIN D RECEPTOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 23098 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1186 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 : 12 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.08 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2662 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1984 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2526 REMARK 3 BIN R VALUE (WORKING SET) : 0.1965 REMARK 3 BIN FREE R VALUE : 0.2347 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.11 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 136 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 : 40 REMARK 3 SOLVENT ATOMS : 191 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.82200 REMARK 3 B22 (A**2) : 4.10020 REMARK 3 B33 (A**2) : -5.92210 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) : 0.213 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.163 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.146 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.152 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.141 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 : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2075 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2811 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 729 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 53 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 288 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2075 ; 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 : 2661 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.66 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.12 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 3W0C 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_1000095725. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-04 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 : 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23148 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 27.863 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : 0.36000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0, 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 22.18500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.04350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.95850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.04350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.18500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.95850 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 61.29 -155.33 REMARK 500 ASP A 342 59.07 -93.79 REMARK 500 ASP A 348 72.18 -103.22 REMARK 500 LEU A 414 -154.24 -100.46 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 6DS A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3W0C RELATED DB: PDB REMARK 900 RELATED ID: 3W0Y RELATED DB: PDB DBREF 3W0C A 120 164 UNP P11473 VDR_HUMAN 120 164 DBREF 3W0C 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 6DS A 501 40 HETNAM 6DS (4S)-4-HYDROXY-5-[2-METHYL-4-(3-{3-METHYL-4-[(1E)-4,4, HETNAM 2 6DS 4-TRIFLUORO-3-HYDROXY-3-(TRIFLUOROMETHYL)BUT-1-EN-1- HETNAM 3 6DS YL]PHENYL}PENTAN-3-YL)PHENOXY]PENTANOIC ACID FORMUL 2 6DS C29 H34 F6 O5 FORMUL 3 HOH *191(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 ASN A 276 1 22 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 379 SER A 405 1 27 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 3.14 SITE 1 AC1 23 THR A 142 TYR A 143 LEU A 227 LEU A 230 SITE 2 AC1 23 ALA A 231 LEU A 233 VAL A 234 SER A 237 SITE 3 AC1 23 LYS A 240 ILE A 271 ARG A 274 SER A 275 SITE 4 AC1 23 TRP A 286 TYR A 295 HIS A 305 HIS A 397 SITE 5 AC1 23 TYR A 401 LEU A 404 LEU A 414 VAL A 418 SITE 6 AC1 23 PHE A 422 HOH A 658 HOH A 683 CRYST1 44.370 51.917 132.087 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 0.022538 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019262 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007571 0.00000