HEADER GENE REGULATION 18-SEP-09 3A78 TITLE CRYSTAL STRUCTURE OF THE HUMAN VDR LIGAND BINDING DOMAIN BOUND TO THE TITLE 2 NATURAL METABOLITE 1ALPHA,25-DIHYDROXY-3-EPI-VITAMIN D3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN; COMPND 5 SYNONYM: VDR, 1,25-DIHYDROXYVITAMIN D3 RECEPTOR, NUCLEAR RECEPTOR COMPND 6 SUBFAMILY 1 GROUP I MEMBER 1; COMPND 7 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS TRANSCRIPTION, GENE REGULATION, DISEASE MUTATION, DNA-BINDING, METAL- KEYWDS 2 BINDING, NUCLEUS, PHOSPHOPROTEIN, RECEPTOR, TRANSCRIPTION KEYWDS 3 REGULATION, ZINC-FINGER EXPDTA X-RAY DIFFRACTION AUTHOR Y.SATO,R.SIGUEIRO,P.ANTONY,N.ROCHEL,D.MORAS REVDAT 3 01-NOV-23 3A78 1 REMARK SEQADV REVDAT 2 16-AUG-17 3A78 1 SOURCE REMARK REVDAT 1 13-OCT-10 3A78 0 JRNL AUTH F.MOLNAR,R.SIGUEIRO,Y.SATO,P.ANTONY,A.MOURINO,N.ROCHEL, JRNL AUTH 2 D.MORAS JRNL TITL STRUCTURAL BASIS OF THE ACTIVATION OF THE HUMAN VITAMIN D JRNL TITL 2 RECEPTOR BY THE NATURAL METABOLITE JRNL TITL 3 1ALPHA,25-DIHYDROXY-3-EPI-VITAMIN D3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 21954 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1169 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1569 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2026 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 369 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : -0.42000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.153 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.794 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2122 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2884 ; 1.130 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 264 ; 4.284 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 86 ;33.790 ;24.186 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 389 ;11.832 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ; 7.502 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 336 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1542 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1212 ; 0.188 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1509 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 322 ; 0.112 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 63 ; 0.157 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 49 ; 0.129 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1337 ; 0.502 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2110 ; 0.858 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 869 ; 1.292 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 768 ; 2.027 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3A78 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000028898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-08 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 : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975531 REMARK 200 MONOCHROMATOR : SI(111) OR SI(311) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23145 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 48.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 11.3000 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 (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : 0.24000 REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5.2.0019 REMARK 200 STARTING MODEL: PDB ENTRY 1DB1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM TRIS, 100MM NACL, 1MM TCEP, 0.05M REMARK 280 MES, 0.7M AMMONIUM SULFATE, PH 6.0, VAPOR DIFFUSION, SITTING REMARK 280 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 22.44450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.09800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.56000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.09800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.44450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.56000 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 114 REMARK 465 SER A 115 REMARK 465 HIS A 116 REMARK 465 MET A 117 REMARK 465 ASN A 424 REMARK 465 GLU A 425 REMARK 465 ILE A 426 REMARK 465 SER A 427 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 119 OG REMARK 480 ARG A 130 CD NE CZ NH1 NH2 REMARK 480 GLN A 347 OE1 NE2 REMARK 480 GLU A 395 CD OE1 OE2 REMARK 480 ARG A 402 CZ NH1 NH2 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 A 402 O HOH A 180 2.14 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 SER A 119 CB SER A 119 OG 0.126 REMARK 500 GLU A 126 C GLU A 127 N 0.247 REMARK 500 ASN A 290 C GLN A 291 N 0.229 REMARK 500 GLN A 291 C ASP A 292 N 0.231 REMARK 500 GLN A 347 CD GLN A 347 OE1 -0.200 REMARK 500 ARG A 402 NE ARG A 402 CZ 0.381 REMARK 500 ARG A 402 CZ ARG A 402 NH2 0.256 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 GLU A 126 C - N - CA ANGL. DEV. = -19.6 DEGREES REMARK 500 GLN A 347 CG - CD - OE1 ANGL. DEV. = -19.8 DEGREES REMARK 500 ARG A 402 NH1 - CZ - NH2 ANGL. DEV. = -11.0 DEGREES REMARK 500 ARG A 402 NE - CZ - NH1 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG A 402 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES 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 51.77 -148.53 REMARK 500 ASP A 283 13.97 -143.93 REMARK 500 ASN A 290 -175.69 -68.10 REMARK 500 ASP A 342 55.90 -107.00 REMARK 500 LEU A 414 -157.56 -99.26 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 GLN A 347 0.13 SIDE CHAIN REMARK 500 ARG A 402 0.32 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 125 12.99 REMARK 500 GLN A 291 -10.25 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 3EV A 428 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DB1 RELATED DB: PDB REMARK 900 1DB1 CONTAINS THE HUMAN VDR LBD BOUND TO 1 ALPHA, 25- REMARK 900 DIHYDROXYVITAMIN D3 (CALCITRIOL) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN HAS BEEN GENETICALLY ENGINEERED TO REMARK 999 LACK RESIDUES 165-215. DBREF 3A78 A 118 164 UNP P11473 VDR_HUMAN 118 164 DBREF 3A78 A 216 427 UNP P11473 VDR_HUMAN 216 427 SEQADV 3A78 GLY A 114 UNP P11473 EXPRESSION TAG SEQADV 3A78 SER A 115 UNP P11473 EXPRESSION TAG SEQADV 3A78 HIS A 116 UNP P11473 EXPRESSION TAG SEQADV 3A78 MET A 117 UNP P11473 EXPRESSION TAG SEQRES 1 A 263 GLY SER HIS MET ASP SER LEU ARG PRO LYS LEU SER GLU SEQRES 2 A 263 GLU GLN GLN ARG ILE ILE ALA ILE LEU LEU ASP ALA HIS SEQRES 3 A 263 HIS LYS THR TYR ASP PRO THR TYR SER ASP PHE CYS GLN SEQRES 4 A 263 PHE ARG PRO PRO VAL ARG VAL ASN ASP GLY GLY GLY SER SEQRES 5 A 263 VAL THR LEU GLU LEU SER GLN LEU SER MET LEU PRO HIS SEQRES 6 A 263 LEU ALA ASP LEU VAL SER TYR SER ILE GLN LYS VAL ILE SEQRES 7 A 263 GLY PHE ALA LYS MET ILE PRO GLY PHE ARG ASP LEU THR SEQRES 8 A 263 SER GLU ASP GLN ILE VAL LEU LEU LYS SER SER ALA ILE SEQRES 9 A 263 GLU VAL ILE MET LEU ARG SER ASN GLU SER PHE THR MET SEQRES 10 A 263 ASP ASP MET SER TRP THR CYS GLY ASN GLN ASP TYR LYS SEQRES 11 A 263 TYR ARG VAL SER ASP VAL THR LYS ALA GLY HIS SER LEU SEQRES 12 A 263 GLU LEU ILE GLU PRO LEU ILE LYS PHE GLN VAL GLY LEU SEQRES 13 A 263 LYS LYS LEU ASN LEU HIS GLU GLU GLU HIS VAL LEU LEU SEQRES 14 A 263 MET ALA ILE CYS ILE VAL SER PRO ASP ARG PRO GLY VAL SEQRES 15 A 263 GLN ASP ALA ALA LEU ILE GLU ALA ILE GLN ASP ARG LEU SEQRES 16 A 263 SER ASN THR LEU GLN THR TYR ILE ARG CYS ARG HIS PRO SEQRES 17 A 263 PRO PRO GLY SER HIS LEU LEU TYR ALA LYS MET ILE GLN SEQRES 18 A 263 LYS LEU ALA ASP LEU ARG SER LEU ASN GLU GLU HIS SER SEQRES 19 A 263 LYS GLN TYR ARG CYS LEU SER PHE GLN PRO GLU CYS SER SEQRES 20 A 263 MET LYS LEU THR PRO LEU VAL LEU GLU VAL PHE GLY ASN SEQRES 21 A 263 GLU ILE SER HET 3EV A 428 30 HET SO4 A 1 5 HET SO4 A 2 5 HETNAM 3EV (1S,3S,5Z,7E,14BETA,17ALPHA)-9,10-SECOCHOLESTA-5,7,10- HETNAM 2 3EV TRIENE-1,3,25-TRIOL HETNAM SO4 SULFATE ION HETSYN 3EV 1ALPHA,25-DIHYDROXY-3-EPI-VITAMIN D3 FORMUL 2 3EV C27 H44 O3 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *369(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 1 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 O TYR A 295 N TRP A 286 CISPEP 1 PRO A 373 PRO A 374 0 -3.90 SITE 1 AC1 14 HOH A 9 TYR A 143 TYR A 147 LEU A 227 SITE 2 AC1 14 VAL A 234 SER A 237 ILE A 271 ARG A 274 SITE 3 AC1 14 SER A 275 SER A 278 TRP A 286 CYS A 288 SITE 4 AC1 14 HIS A 305 HIS A 397 SITE 1 AC2 8 HOH A 56 HOH A 184 PRO A 408 GLU A 409 SITE 2 AC2 8 CYS A 410 SER A 411 HOH A 458 HOH A 498 SITE 1 AC3 3 THR A 280 MET A 281 LYS A 321 CRYST1 44.889 51.120 132.196 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 0.022277 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007565 0.00000