HEADER TRANSCRIPTION/DNA 05-NOV-01 1KB4 TITLE CRYSTAL STRUCTURE OF VDR DNA-BINDING DOMAIN BOUND TO A CANONICAL TITLE 2 DIRECT REPEAT WITH THREE BASE PAIR SPACER (DR3) RESPONSE ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*AP*CP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*A) COMPND 3 -3'; COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CANONICAL DIRECT REPEAT WITH 3 BASE PAIR SPACER (DR3) COMPND 7 RESPONSE ELEMENT; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*GP*TP*G) COMPND 10 -3'; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: CANONICAL DIRECT REPEAT WITH 3 BASE PAIR SPACER (DR3) COMPND 14 RESPONSE ELEMENT; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: VITAMIN D3 RECEPTOR; COMPND 17 CHAIN: A, B; COMPND 18 FRAGMENT: DNA-BINDING DOMAIN (RESIDUES 16-125); COMPND 19 SYNONYM: VDR, 1,25-DIHYDROXYVITAMIN D3 RECEPTOR; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: VDR; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PET11A-VDR-N1-RPLKS KEYWDS VDR, NUCLEAR RECEPTOR, PROTEIN-DNA COMPLEX, VITAMIN D, TRANSCRIPTION- KEYWDS 2 DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.L.SHAFFER,D.T.GEWIRTH REVDAT 3 16-AUG-23 1KB4 1 REMARK LINK REVDAT 2 24-FEB-09 1KB4 1 VERSN REVDAT 1 03-MAY-02 1KB4 0 JRNL AUTH P.L.SHAFFER,D.T.GEWIRTH JRNL TITL STRUCTURAL BASIS OF VDR-DNA INTERACTIONS ON DIRECT REPEAT JRNL TITL 2 RESPONSE ELEMENTS. JRNL REF EMBO J. V. 21 2242 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 11980721 JRNL DOI 10.1093/EMBOJ/21.9.2242 REMARK 2 REMARK 2 RESOLUTION. 2.80 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 : MAXIMUM LIKELIHOOD FUNCTION REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 464135.500 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 11200 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) : 0.214 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1124 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.90 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 828 REMARK 3 BIN R VALUE (WORKING SET) : 0.4720 REMARK 3 BIN FREE R VALUE : 0.4860 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 81 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.054 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1468 REMARK 3 NUCLEIC ACID ATOMS : 732 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 79.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 24.32000 REMARK 3 B22 (A**2) : 24.32000 REMARK 3 B33 (A**2) : -48.64000 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) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.64 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.78 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.310 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.080 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.910 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.540 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.530 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 37.59 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : PARAM_ZN REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KB4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014771. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APS-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12384 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: TR HALF-COMPLEX FROM PDB ENTRY 2NLL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM CHLORIDE, MES, REMARK 280 GLYCEROL, DTT, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 120.98500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.75000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 181.47750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.75000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.49250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.75000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.75000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 181.47750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.75000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.75000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.49250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 120.98500 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, B 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 PHE A 16 REMARK 465 ASP A 17 REMARK 465 ARG A 18 REMARK 465 ASN A 19 REMARK 465 VAL A 20 REMARK 465 PRO A 21 REMARK 465 ALA 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 LYS A 123 REMARK 465 LEU A 124 REMARK 465 SER A 125 REMARK 465 PHE B 216 REMARK 465 ASP B 217 REMARK 465 ARG B 218 REMARK 465 ASN B 219 REMARK 465 VAL B 220 REMARK 465 PRO B 221 REMARK 465 ARG B 321 REMARK 465 PRO B 322 REMARK 465 LYS B 323 REMARK 465 LEU B 324 REMARK 465 SER B 325 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 ARG A 30 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 101 CG CD OE1 NE2 REMARK 470 ARG A 110 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 GLU A 112 CG CD OE1 OE2 REMARK 470 GLU A 114 CG CD OE1 OE2 REMARK 470 ARG B 230 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 267 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 302 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 303 CG CD CE NZ REMARK 470 ARG B 304 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 305 CG CD OE1 OE2 REMARK 470 MET B 306 CG SD CE REMARK 470 LYS B 309 CG CD CE NZ REMARK 470 ARG B 310 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 312 CG CD OE1 OE2 REMARK 470 GLU B 313 CG CD OE1 OE2 REMARK 470 GLU B 314 CG CD OE1 OE2 REMARK 470 LYS B 317 CG CD CE NZ REMARK 470 ASP B 318 CG OD1 OD2 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 NH1 ARG B 250 O HOH B 630 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 CYS B 260 CB CYS B 260 SG -0.099 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 LYS A 55 15.78 54.49 REMARK 500 PHE A 62 -119.01 -104.91 REMARK 500 ASP A 65 41.55 -152.02 REMARK 500 LYS A 70 -38.18 -39.25 REMARK 500 ARG A 104 25.09 -72.54 REMARK 500 LYS A 111 -69.97 -97.47 REMARK 500 GLU A 112 32.21 -64.01 REMARK 500 GLU A 113 18.16 -146.46 REMARK 500 PHE B 262 -122.20 -112.90 REMARK 500 ASN B 263 -70.31 -79.67 REMARK 500 ASP B 265 56.96 -156.13 REMARK 500 MET B 306 13.65 -55.74 REMARK 500 ASP B 318 39.37 -90.70 REMARK 500 SER B 319 -48.80 -137.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC C 401 0.07 SIDE CHAIN REMARK 500 DG C 414 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 150 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 CYS A 27 SG 113.3 REMARK 620 3 CYS A 41 SG 107.4 99.1 REMARK 620 4 CYS A 44 SG 122.9 110.9 99.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 151 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 60 SG REMARK 620 2 CYS A 66 SG 104.8 REMARK 620 3 CYS A 76 SG 104.0 107.7 REMARK 620 4 CYS A 79 SG 116.6 107.8 115.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 350 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 224 SG REMARK 620 2 CYS B 227 SG 113.1 REMARK 620 3 CYS B 241 SG 106.6 105.7 REMARK 620 4 CYS B 244 SG 115.2 111.8 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 351 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 260 SG REMARK 620 2 CYS B 266 SG 131.0 REMARK 620 3 CYS B 276 SG 94.3 104.5 REMARK 620 4 CYS B 279 SG 111.2 111.2 96.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 351 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KB2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VDR DNA-BINDING DOMAIN BOUND TO MOUSE REMARK 900 OSTEOPONTIN (SPP) RESPONSE ELEMENT REMARK 900 RELATED ID: 1KB6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VDR DNA-BINDING DOMAIN BOUND TO RAT REMARK 900 OSTEOCALCIN (OC) RESPONSE ELEMENT DBREF 1KB4 A 16 125 UNP P11473 VDR_HUMAN 16 125 DBREF 1KB4 B 216 325 UNP P11473 VDR_HUMAN 16 125 DBREF 1KB4 C 401 418 PDB 1KB4 1KB4 401 418 DBREF 1KB4 D 419 436 PDB 1KB4 1KB4 419 436 SEQRES 1 C 18 DC DA DC DA DG DG DT DC DA DC DG DA DA SEQRES 2 C 18 DG DG DT DC DA SEQRES 1 D 18 DT DG DA DC DC DT DT DC DG DT DG DA DC SEQRES 2 D 18 DC DT DG DT DG SEQRES 1 A 110 PHE ASP ARG ASN VAL PRO ARG ILE CYS GLY VAL CYS GLY SEQRES 2 A 110 ASP ARG ALA THR GLY PHE HIS PHE ASN ALA MET THR CYS SEQRES 3 A 110 GLU GLY CYS LYS GLY PHE PHE ARG ARG SER MET LYS ARG SEQRES 4 A 110 LYS ALA LEU PHE THR CYS PRO PHE ASN GLY ASP CYS ARG SEQRES 5 A 110 ILE THR LYS ASP ASN ARG ARG HIS CYS GLN ALA CYS ARG SEQRES 6 A 110 LEU LYS ARG CYS VAL ASP ILE GLY MET MET LYS GLU PHE SEQRES 7 A 110 ILE LEU THR ASP GLU GLU VAL GLN ARG LYS ARG GLU MET SEQRES 8 A 110 ILE LEU LYS ARG LYS GLU GLU GLU ALA LEU LYS ASP SER SEQRES 9 A 110 LEU ARG PRO LYS LEU SER SEQRES 1 B 110 PHE ASP ARG ASN VAL PRO ARG ILE CYS GLY VAL CYS GLY SEQRES 2 B 110 ASP ARG ALA THR GLY PHE HIS PHE ASN ALA MET THR CYS SEQRES 3 B 110 GLU GLY CYS LYS GLY PHE PHE ARG ARG SER MET LYS ARG SEQRES 4 B 110 LYS ALA LEU PHE THR CYS PRO PHE ASN GLY ASP CYS ARG SEQRES 5 B 110 ILE THR LYS ASP ASN ARG ARG HIS CYS GLN ALA CYS ARG SEQRES 6 B 110 LEU LYS ARG CYS VAL ASP ILE GLY MET MET LYS GLU PHE SEQRES 7 B 110 ILE LEU THR ASP GLU GLU VAL GLN ARG LYS ARG GLU MET SEQRES 8 B 110 ILE LEU LYS ARG LYS GLU GLU GLU ALA LEU LYS ASP SER SEQRES 9 B 110 LEU ARG PRO LYS LEU SER HET ZN A 150 1 HET ZN A 151 1 HET ZN B 350 1 HET ZN B 351 1 HETNAM ZN ZINC ION FORMUL 5 ZN 4(ZN 2+) FORMUL 9 HOH *31(H2 O) HELIX 1 1 CYS A 41 ARG A 54 1 14 HELIX 2 2 ASN A 72 HIS A 75 5 4 HELIX 3 3 CYS A 76 ILE A 87 1 12 HELIX 4 4 MET A 90 ILE A 94 5 5 HELIX 5 5 THR A 96 ARG A 104 1 9 HELIX 6 6 CYS B 241 LYS B 255 1 15 HELIX 7 7 ASP B 271 HIS B 275 5 5 HELIX 8 8 CYS B 276 GLY B 288 1 13 HELIX 9 9 MET B 290 ILE B 294 5 5 HELIX 10 10 THR B 296 MET B 306 1 11 HELIX 11 11 LYS B 309 LYS B 317 1 9 SHEET 1 A 2 PHE A 34 HIS A 35 0 SHEET 2 A 2 ALA A 38 MET A 39 -1 O ALA A 38 N HIS A 35 SHEET 1 B 2 GLY B 233 HIS B 235 0 SHEET 2 B 2 ALA B 238 THR B 240 -1 O ALA B 238 N HIS B 235 LINK SG CYS A 24 ZN ZN A 150 1555 1555 2.16 LINK SG CYS A 27 ZN ZN A 150 1555 1555 2.29 LINK SG CYS A 41 ZN ZN A 150 1555 1555 2.46 LINK SG CYS A 44 ZN ZN A 150 1555 1555 2.36 LINK SG CYS A 60 ZN ZN A 151 1555 1555 2.30 LINK SG CYS A 66 ZN ZN A 151 1555 1555 2.38 LINK SG CYS A 76 ZN ZN A 151 1555 1555 2.21 LINK SG CYS A 79 ZN ZN A 151 1555 1555 2.19 LINK SG CYS B 224 ZN ZN B 350 1555 1555 2.25 LINK SG CYS B 227 ZN ZN B 350 1555 1555 2.21 LINK SG CYS B 241 ZN ZN B 350 1555 1555 2.54 LINK SG CYS B 244 ZN ZN B 350 1555 1555 2.34 LINK SG CYS B 260 ZN ZN B 351 1555 1555 2.18 LINK SG CYS B 266 ZN ZN B 351 1555 1555 2.37 LINK SG CYS B 276 ZN ZN B 351 1555 1555 2.50 LINK SG CYS B 279 ZN ZN B 351 1555 1555 2.35 SITE 1 AC1 4 CYS A 24 CYS A 27 CYS A 41 CYS A 44 SITE 1 AC2 4 CYS A 60 CYS A 66 CYS A 76 CYS A 79 SITE 1 AC3 4 CYS B 224 CYS B 227 CYS B 241 CYS B 244 SITE 1 AC4 4 CYS B 260 CYS B 266 CYS B 276 CYS B 279 CRYST1 61.500 61.500 241.970 90.00 90.00 90.00 P 43 21 2 16 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 0.016261 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016261 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004133 0.00000