PDB Short entry for 1J7E HEADER TRANSPORT, LIGAND BINDING PROTEIN 16-MAY-01 1J7E TITLE A STRUCTURAL BASIS FOR THE UNIQUE BINDING FEATURES OF THE HUMAN TITLE 2 VITAMIN D-BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D BINDING PROTEIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS VITAMIN D BINDING, VITAMIN D3 ANALOGUE, GROUP-SPECIFIC COMPONENT, GC- KEYWDS 2 GLOBULIN, TRANSPORT, LIGAND BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.VERBOVEN,A.RABIJNS,M.DE MAEYER,H.VAN BAELEN,R.BOUILLON,C.DE RANTER REVDAT 4 16-AUG-23 1J7E 1 REMARK SEQADV REVDAT 3 31-JAN-18 1J7E 1 REMARK REVDAT 2 24-FEB-09 1J7E 1 VERSN REVDAT 1 06-FEB-02 1J7E 0 JRNL AUTH C.VERBOVEN,A.RABIJNS,M.DE MAEYER,H.VAN BAELEN,R.BOUILLON, JRNL AUTH 2 C.DE RANTER JRNL TITL A STRUCTURAL BASIS FOR THE UNIQUE BINDING FEATURES OF THE JRNL TITL 2 HUMAN VITAMIN D-BINDING PROTEIN. JRNL REF NAT.STRUCT.BIOL. V. 9 131 2002 JRNL REFN ISSN 1072-8368 JRNL PMID 11799400 JRNL DOI 10.1038/NSB754 REMARK 2 REMARK 2 RESOLUTION. 2.55 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 664800.240 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 39559 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) : 0.213 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1925 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4583 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 153 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6804 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 120 REMARK 3 SOLVENT ATOMS : 246 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.55000 REMARK 3 B22 (A**2) : -1.55000 REMARK 3 B33 (A**2) : 3.10000 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) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.950 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) : 3.950 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.600 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.100 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.730 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 46.04 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 : JY.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : JY.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT: CHAIN A AND B. FOR REMARK 3 CHAIN REMARK 3 A RESIDUES 1-6, 60-68, 81-83, 99-102 AND 458 AND FOR CHAIN B REMARK 3 RESIDUES REMARK 3 1-2, 98-104, AND 457-458 ARE DISORDERED AND HAVE NOT BEEN REMARK 3 INCLUDED IN THE MODEL. REMARK 4 REMARK 4 1J7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013452. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.912 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : TOROIDAL MIRROR 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 : 51580 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : 0.07700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.53900 REMARK 200 R SYM FOR SHELL (I) : 0.53900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: 1J78 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, SODIUM ACETATE, PH 4.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 20K, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 36.71000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.06500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.35500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 LEU A 1 REMARK 465 GLU A 2 REMARK 465 ARG A 3 REMARK 465 GLY A 4 REMARK 465 ARG A 5 REMARK 465 ASP A 6 REMARK 465 ALA A 60 REMARK 465 GLU A 61 REMARK 465 GLY A 62 REMARK 465 ALA A 63 REMARK 465 ASP A 64 REMARK 465 PRO A 65 REMARK 465 ASP A 66 REMARK 465 CYS A 67 REMARK 465 TYR A 68 REMARK 465 GLU A 81 REMARK 465 SER A 82 REMARK 465 ASN A 83 REMARK 465 GLU A 99 REMARK 465 GLY A 100 REMARK 465 LEU A 101 REMARK 465 GLU A 102 REMARK 465 LEU A 458 REMARK 465 LEU B 1 REMARK 465 GLU B 2 REMARK 465 LYS B 98 REMARK 465 GLU B 99 REMARK 465 GLY B 100 REMARK 465 LEU B 101 REMARK 465 GLU B 102 REMARK 465 ARG B 103 REMARK 465 LYS B 104 REMARK 465 ILE B 457 REMARK 465 LEU B 458 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 ASN A 10 CG OD1 ND2 REMARK 470 LYS A 14 CG CD CE NZ REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 ARG B 3 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 5 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 10 CG OD1 ND2 REMARK 470 LYS B 11 CG CD CE NZ REMARK 470 LYS B 14 CG CD CE NZ REMARK 470 ASP B 64 CG OD1 OD2 REMARK 470 LYS B 78 CB CG CD CE NZ REMARK 470 GLU B 94 CG CD OE1 OE2 REMARK 470 LEU B 105 CG CD1 CD2 REMARK 470 LYS B 111 CG CD CE NZ REMARK 470 LYS B 134 CG CD CE NZ REMARK 470 GLU B 306 CG CD OE1 OE2 REMARK 470 ASP B 361 CG OD1 OD2 REMARK 470 GLU B 363 CG CD OE1 OE2 REMARK 470 LYS B 377 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 574 O HOH A 606 3654 2.03 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 CYS A 106 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 CYS A 257 CA - CB - SG ANGL. DEV. = 8.0 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 PHE A 36 78.38 -119.80 REMARK 500 CYS A 58 29.97 -75.15 REMARK 500 LYS A 104 -18.08 68.57 REMARK 500 LEU A 105 47.86 -80.87 REMARK 500 ALA A 108 -2.74 -59.96 REMARK 500 GLU A 286 153.18 -47.12 REMARK 500 GLU A 306 85.95 50.87 REMARK 500 LYS A 316 -16.80 -46.64 REMARK 500 CYS A 360 -60.59 -91.04 REMARK 500 ASP A 361 47.19 -84.84 REMARK 500 ASP A 393 -12.46 78.62 REMARK 500 ASN A 440 52.70 -118.07 REMARK 500 LYS B 11 -79.05 -48.69 REMARK 500 PHE B 36 79.32 -116.20 REMARK 500 ALA B 57 31.52 -89.42 REMARK 500 CYS B 58 -16.38 -143.04 REMARK 500 PRO B 65 -16.83 -48.81 REMARK 500 CYS B 67 -80.08 -5.68 REMARK 500 TYR B 68 -78.07 -44.94 REMARK 500 SER B 82 -8.90 -59.09 REMARK 500 ASN B 83 58.46 -141.24 REMARK 500 MET B 107 33.43 -70.13 REMARK 500 ASP B 135 86.15 -157.15 REMARK 500 PRO B 228 9.73 -66.34 REMARK 500 LEU B 232 -48.82 -27.63 REMARK 500 LEU B 307 -172.79 -61.63 REMARK 500 CYS B 360 -74.60 -90.45 REMARK 500 THR B 366 31.62 -64.21 REMARK 500 THR B 367 -36.64 -146.10 REMARK 500 ASP B 393 -12.95 75.05 REMARK 500 LYS B 455 14.67 -66.68 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 TYR A 210 0.06 SIDE CHAIN 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 JY A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JY B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA B 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J78 RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC ANALYSIS OF THE VITAMIN D BINDING PROTEIN DBREF 1J7E A 1 458 UNP P02774 VTDB_HUMAN 17 474 DBREF 1J7E B 1 458 UNP P02774 VTDB_HUMAN 17 474 SEQADV 1J7E THR A 420 UNP P02774 LYS 436 VARIANT SEQADV 1J7E THR B 420 UNP P02774 LYS 436 VARIANT SEQRES 1 A 458 LEU GLU ARG GLY ARG ASP TYR GLU LYS ASN LYS VAL CYS SEQRES 2 A 458 LYS GLU PHE SER HIS LEU GLY LYS GLU ASP PHE THR SER SEQRES 3 A 458 LEU SER LEU VAL LEU TYR SER ARG LYS PHE PRO SER GLY SEQRES 4 A 458 THR PHE GLU GLN VAL SER GLN LEU VAL LYS GLU VAL VAL SEQRES 5 A 458 SER LEU THR GLU ALA CYS CYS ALA GLU GLY ALA ASP PRO SEQRES 6 A 458 ASP CYS TYR ASP THR ARG THR SER ALA LEU SER ALA LYS SEQRES 7 A 458 SER CYS GLU SER ASN SER PRO PHE PRO VAL HIS PRO GLY SEQRES 8 A 458 THR ALA GLU CYS CYS THR LYS GLU GLY LEU GLU ARG LYS SEQRES 9 A 458 LEU CYS MET ALA ALA LEU LYS HIS GLN PRO GLN GLU PHE SEQRES 10 A 458 PRO THR TYR VAL GLU PRO THR ASN ASP GLU ILE CYS GLU SEQRES 11 A 458 ALA PHE ARG LYS ASP PRO LYS GLU TYR ALA ASN GLN PHE SEQRES 12 A 458 MET TRP GLU TYR SER THR ASN TYR GLY GLN ALA PRO LEU SEQRES 13 A 458 SER LEU LEU VAL SER TYR THR LYS SER TYR LEU SER MET SEQRES 14 A 458 VAL GLY SER CYS CYS THR SER ALA SER PRO THR VAL CYS SEQRES 15 A 458 PHE LEU LYS GLU ARG LEU GLN LEU LYS HIS LEU SER LEU SEQRES 16 A 458 LEU THR THR LEU SER ASN ARG VAL CYS SER GLN TYR ALA SEQRES 17 A 458 ALA TYR GLY GLU LYS LYS SER ARG LEU SER ASN LEU ILE SEQRES 18 A 458 LYS LEU ALA GLN LYS VAL PRO THR ALA ASP LEU GLU ASP SEQRES 19 A 458 VAL LEU PRO LEU ALA GLU ASP ILE THR ASN ILE LEU SER SEQRES 20 A 458 LYS CYS CYS GLU SER ALA SER GLU ASP CYS MET ALA LYS SEQRES 21 A 458 GLU LEU PRO GLU HIS THR VAL LYS LEU CYS ASP ASN LEU SEQRES 22 A 458 SER THR LYS ASN SER LYS PHE GLU ASP CYS CYS GLN GLU SEQRES 23 A 458 LYS THR ALA MET ASP VAL PHE VAL CYS THR TYR PHE MET SEQRES 24 A 458 PRO ALA ALA GLN LEU PRO GLU LEU PRO ASP VAL GLU LEU SEQRES 25 A 458 PRO THR ASN LYS ASP VAL CYS ASP PRO GLY ASN THR LYS SEQRES 26 A 458 VAL MET ASP LYS TYR THR PHE GLU LEU SER ARG ARG THR SEQRES 27 A 458 HIS LEU PRO GLU VAL PHE LEU SER LYS VAL LEU GLU PRO SEQRES 28 A 458 THR LEU LYS SER LEU GLY GLU CYS CYS ASP VAL GLU ASP SEQRES 29 A 458 SER THR THR CYS PHE ASN ALA LYS GLY PRO LEU LEU LYS SEQRES 30 A 458 LYS GLU LEU SER SER PHE ILE ASP LYS GLY GLN GLU LEU SEQRES 31 A 458 CYS ALA ASP TYR SER GLU ASN THR PHE THR GLU TYR LYS SEQRES 32 A 458 LYS LYS LEU ALA GLU ARG LEU LYS ALA LYS LEU PRO ASP SEQRES 33 A 458 ALA THR PRO THR GLU LEU ALA LYS LEU VAL ASN LYS ARG SEQRES 34 A 458 SER ASP PHE ALA SER ASN CYS CYS SER ILE ASN SER PRO SEQRES 35 A 458 PRO LEU TYR CYS ASP SER GLU ILE ASP ALA GLU LEU LYS SEQRES 36 A 458 ASN ILE LEU SEQRES 1 B 458 LEU GLU ARG GLY ARG ASP TYR GLU LYS ASN LYS VAL CYS SEQRES 2 B 458 LYS GLU PHE SER HIS LEU GLY LYS GLU ASP PHE THR SER SEQRES 3 B 458 LEU SER LEU VAL LEU TYR SER ARG LYS PHE PRO SER GLY SEQRES 4 B 458 THR PHE GLU GLN VAL SER GLN LEU VAL LYS GLU VAL VAL SEQRES 5 B 458 SER LEU THR GLU ALA CYS CYS ALA GLU GLY ALA ASP PRO SEQRES 6 B 458 ASP CYS TYR ASP THR ARG THR SER ALA LEU SER ALA LYS SEQRES 7 B 458 SER CYS GLU SER ASN SER PRO PHE PRO VAL HIS PRO GLY SEQRES 8 B 458 THR ALA GLU CYS CYS THR LYS GLU GLY LEU GLU ARG LYS SEQRES 9 B 458 LEU CYS MET ALA ALA LEU LYS HIS GLN PRO GLN GLU PHE SEQRES 10 B 458 PRO THR TYR VAL GLU PRO THR ASN ASP GLU ILE CYS GLU SEQRES 11 B 458 ALA PHE ARG LYS ASP PRO LYS GLU TYR ALA ASN GLN PHE SEQRES 12 B 458 MET TRP GLU TYR SER THR ASN TYR GLY GLN ALA PRO LEU SEQRES 13 B 458 SER LEU LEU VAL SER TYR THR LYS SER TYR LEU SER MET SEQRES 14 B 458 VAL GLY SER CYS CYS THR SER ALA SER PRO THR VAL CYS SEQRES 15 B 458 PHE LEU LYS GLU ARG LEU GLN LEU LYS HIS LEU SER LEU SEQRES 16 B 458 LEU THR THR LEU SER ASN ARG VAL CYS SER GLN TYR ALA SEQRES 17 B 458 ALA TYR GLY GLU LYS LYS SER ARG LEU SER ASN LEU ILE SEQRES 18 B 458 LYS LEU ALA GLN LYS VAL PRO THR ALA ASP LEU GLU ASP SEQRES 19 B 458 VAL LEU PRO LEU ALA GLU ASP ILE THR ASN ILE LEU SER SEQRES 20 B 458 LYS CYS CYS GLU SER ALA SER GLU ASP CYS MET ALA LYS SEQRES 21 B 458 GLU LEU PRO GLU HIS THR VAL LYS LEU CYS ASP ASN LEU SEQRES 22 B 458 SER THR LYS ASN SER LYS PHE GLU ASP CYS CYS GLN GLU SEQRES 23 B 458 LYS THR ALA MET ASP VAL PHE VAL CYS THR TYR PHE MET SEQRES 24 B 458 PRO ALA ALA GLN LEU PRO GLU LEU PRO ASP VAL GLU LEU SEQRES 25 B 458 PRO THR ASN LYS ASP VAL CYS ASP PRO GLY ASN THR LYS SEQRES 26 B 458 VAL MET ASP LYS TYR THR PHE GLU LEU SER ARG ARG THR SEQRES 27 B 458 HIS LEU PRO GLU VAL PHE LEU SER LYS VAL LEU GLU PRO SEQRES 28 B 458 THR LEU LYS SER LEU GLY GLU CYS CYS ASP VAL GLU ASP SEQRES 29 B 458 SER THR THR CYS PHE ASN ALA LYS GLY PRO LEU LEU LYS SEQRES 30 B 458 LYS GLU LEU SER SER PHE ILE ASP LYS GLY GLN GLU LEU SEQRES 31 B 458 CYS ALA ASP TYR SER GLU ASN THR PHE THR GLU TYR LYS SEQRES 32 B 458 LYS LYS LEU ALA GLU ARG LEU LYS ALA LYS LEU PRO ASP SEQRES 33 B 458 ALA THR PRO THR GLU LEU ALA LYS LEU VAL ASN LYS ARG SEQRES 34 B 458 SER ASP PHE ALA SER ASN CYS CYS SER ILE ASN SER PRO SEQRES 35 B 458 PRO LEU TYR CYS ASP SER GLU ILE ASP ALA GLU LEU LYS SEQRES 36 B 458 ASN ILE LEU HET JY A 501 30 HET OLA A 502 20 HET JY B 502 30 HET OLA B 503 20 HET OLA B 504 20 HETNAM JY 3-(2-{4-[2-(5-HYDROXY-2-METHYLENE-CYCLOHEXYLIDENE)- HETNAM 2 JY ETHYLIDENE]-7A-METHYL-OCTAHYDRO-INDEN-1-YL}-PROPYL)- HETNAM 3 JY PHENOL HETNAM OLA OLEIC ACID HETSYN JY 22-(M-HYDROXYPHENYL)-23,24,25,26,27-PENTANOR VITAMIN D3 FORMUL 3 JY 2(C28 H38 O2) FORMUL 4 OLA 3(C18 H34 O2) FORMUL 8 HOH *246(H2 O) HELIX 1 1 TYR A 7 LYS A 9 5 3 HELIX 2 2 ASN A 10 PHE A 36 1 27 HELIX 3 3 THR A 40 CYS A 58 1 19 HELIX 4 4 ARG A 71 SER A 79 1 9 HELIX 5 5 GLY A 91 CYS A 96 1 6 HELIX 6 6 CYS A 106 LEU A 110 5 5 HELIX 7 7 THR A 124 ASP A 135 1 12 HELIX 8 8 ASP A 135 TYR A 151 1 17 HELIX 9 9 PRO A 155 CYS A 174 1 20 HELIX 10 10 SER A 178 VAL A 227 1 50 HELIX 11 11 ASP A 231 CYS A 250 1 20 HELIX 12 12 CYS A 257 SER A 274 1 18 HELIX 13 13 ASN A 277 CYS A 284 1 8 HELIX 14 14 THR A 288 MET A 299 1 12 HELIX 15 15 ASN A 315 ASP A 320 5 6 HELIX 16 16 THR A 324 ARG A 336 1 13 HELIX 17 17 PRO A 341 GLY A 357 1 17 HELIX 18 18 GLU A 358 CYS A 360 5 3 HELIX 19 19 ASP A 364 CYS A 391 1 28 HELIX 20 20 THR A 398 LEU A 414 1 17 HELIX 21 21 THR A 418 CYS A 437 1 20 HELIX 22 22 PRO A 442 LYS A 455 1 14 HELIX 23 23 GLU B 8 PHE B 36 1 29 HELIX 24 24 THR B 40 ALA B 60 1 21 HELIX 25 25 ASP B 66 SER B 79 1 14 HELIX 26 26 THR B 92 CYS B 96 5 5 HELIX 27 27 THR B 124 ASP B 135 1 12 HELIX 28 28 ASP B 135 TYR B 151 1 17 HELIX 29 29 PRO B 155 CYS B 174 1 20 HELIX 30 30 SER B 178 GLY B 211 1 34 HELIX 31 31 GLY B 211 VAL B 227 1 17 HELIX 32 32 ASP B 231 CYS B 250 1 20 HELIX 33 33 ASP B 256 SER B 274 1 19 HELIX 34 34 ASN B 277 CYS B 284 1 8 HELIX 35 35 THR B 288 PHE B 298 1 11 HELIX 36 36 ASN B 315 ASP B 320 5 6 HELIX 37 37 THR B 324 ARG B 336 1 13 HELIX 38 38 PRO B 341 GLU B 358 1 18 HELIX 39 39 ASP B 364 CYS B 391 1 28 HELIX 40 40 THR B 398 LEU B 414 1 17 HELIX 41 41 THR B 418 CYS B 437 1 20 HELIX 42 42 PRO B 442 LYS B 455 1 14 SSBOND 1 CYS A 13 CYS A 59 1555 1555 2.03 SSBOND 2 CYS A 80 CYS A 96 1555 1555 2.03 SSBOND 3 CYS A 95 CYS A 106 1555 1555 2.03 SSBOND 4 CYS A 129 CYS A 174 1555 1555 2.04 SSBOND 5 CYS A 173 CYS A 182 1555 1555 2.03 SSBOND 6 CYS A 204 CYS A 250 1555 1555 2.03 SSBOND 7 CYS A 249 CYS A 257 1555 1555 2.04 SSBOND 8 CYS A 270 CYS A 284 1555 1555 2.03 SSBOND 9 CYS A 283 CYS A 295 1555 1555 2.03 SSBOND 10 CYS A 319 CYS A 360 1555 1555 2.03 SSBOND 11 CYS A 359 CYS A 368 1555 1555 2.03 SSBOND 12 CYS A 391 CYS A 437 1555 1555 2.03 SSBOND 13 CYS A 436 CYS A 446 1555 1555 2.03 SSBOND 14 CYS B 13 CYS B 59 1555 1555 2.03 SSBOND 15 CYS B 58 CYS B 67 1555 1555 2.03 SSBOND 16 CYS B 80 CYS B 96 1555 1555 2.03 SSBOND 17 CYS B 95 CYS B 106 1555 1555 2.03 SSBOND 18 CYS B 129 CYS B 174 1555 1555 2.03 SSBOND 19 CYS B 173 CYS B 182 1555 1555 2.04 SSBOND 20 CYS B 204 CYS B 250 1555 1555 2.03 SSBOND 21 CYS B 249 CYS B 257 1555 1555 2.03 SSBOND 22 CYS B 270 CYS B 284 1555 1555 2.03 SSBOND 23 CYS B 283 CYS B 295 1555 1555 2.02 SSBOND 24 CYS B 319 CYS B 360 1555 1555 2.03 SSBOND 25 CYS B 359 CYS B 368 1555 1555 2.03 SSBOND 26 CYS B 391 CYS B 437 1555 1555 2.03 SSBOND 27 CYS B 436 CYS B 446 1555 1555 2.02 SITE 1 AC1 14 GLU A 8 VAL A 12 GLU A 15 SER A 28 SITE 2 AC1 14 LEU A 31 TYR A 32 LYS A 35 LEU A 75 SITE 3 AC1 14 SER A 76 SER A 79 MET A 107 HOH A 521 SITE 4 AC1 14 ASP B 364 THR B 367 SITE 1 AC2 11 GLU B 8 GLU B 15 LEU B 27 SER B 28 SITE 2 AC2 11 TYR B 32 PHE B 36 LEU B 47 TYR B 68 SITE 3 AC2 11 SER B 76 SER B 79 MET B 107 SITE 1 AC3 7 VAL A 348 GLU A 350 PRO A 351 LYS A 354 SITE 2 AC3 7 GLU A 379 PHE A 383 ASP A 451 SITE 1 AC4 1 GLU B 379 SITE 1 AC5 6 ASP A 361 ALA B 208 ALA B 209 TYR B 210 SITE 2 AC5 6 LYS B 214 LEU B 444 CRYST1 131.977 131.977 73.420 90.00 90.00 90.00 P 43 8 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 0.007577 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007577 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013620 0.00000