HEADER TRANSPORT PROTEIN 30-MAR-06 2GJ5 TITLE CRYSTAL STRUCTURE OF A SECONDARY VITAMIN D3 BINDING SITE OF TITLE 2 MILK BETA-LACTOGLOBULIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTOGLOBULIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-LG, ALLERGEN BOS D 5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS BETA-LACTOGLOBULIN, VITAMIN D3, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.C.YANG,H.H.GUAN,M.Y.LIU,J.M.YANG,W.L.CHEN,C.J.CHEN,S.J.MAO REVDAT 3 20-OCT-09 2GJ5 1 JRNL REVDAT 2 24-FEB-09 2GJ5 1 VERSN REVDAT 1 02-OCT-07 2GJ5 0 JRNL AUTH M.C.YANG,H.H.GUAN,M.Y.LIU,Y.H.LIN,J.M.YANG, JRNL AUTH 2 W.L.CHEN,C.J.CHEN,S.J.MAO JRNL TITL CRYSTAL STRUCTURE OF A SECONDARY VITAMIN D3 BINDING JRNL TITL 2 SITE OF MILK BETA-LACTOGLOBULIN. JRNL REF PROTEINS V. 71 1197 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18004750 JRNL DOI 10.1002/PROT.21811 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 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 : 7191 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 551 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 : 1272 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 38 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.28 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 2GJ5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-06. REMARK 100 THE RCSB ID CODE IS RCSB037182. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL12B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7671 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03800 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 2BLG 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: 0.1M HEPES, 1.4M TRI-SODIUM CITRATE REMARK 280 DEHYDRATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.38533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.19267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.19267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.38533 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 LEU A 1 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 33 -94.61 -42.62 REMARK 500 ASN A 63 -135.01 62.55 REMARK 500 PRO A 79 -18.93 -46.10 REMARK 500 THR A 97 145.14 -170.37 REMARK 500 TYR A 99 -44.51 64.26 REMARK 500 ALA A 111 -157.01 -134.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 177 DISTANCE = 11.78 ANGSTROMS REMARK 525 HOH A 178 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 179 DISTANCE = 7.72 ANGSTROMS REMARK 525 HOH A 180 DISTANCE = 10.35 ANGSTROMS REMARK 525 HOH A 181 DISTANCE = 5.19 ANGSTROMS REMARK 525 HOH A 183 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A 188 DISTANCE = 5.27 ANGSTROMS REMARK 525 HOH A 192 DISTANCE = 9.40 ANGSTROMS REMARK 525 HOH A 193 DISTANCE = 5.64 ANGSTROMS REMARK 525 HOH A 194 DISTANCE = 5.73 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VD3 A 163 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VD3 A 164 DBREF 2GJ5 A 1 162 UNP P02754 LACB_BOVIN 17 178 SEQRES 1 A 162 LEU ILE VAL THR GLN THR MET LYS GLY LEU ASP ILE GLN SEQRES 2 A 162 LYS VAL ALA GLY THR TRP TYR SER LEU ALA MET ALA ALA SEQRES 3 A 162 SER ASP ILE SER LEU LEU ASP ALA GLN SER ALA PRO LEU SEQRES 4 A 162 ARG VAL TYR VAL GLU GLU LEU LYS PRO THR PRO GLU GLY SEQRES 5 A 162 ASP LEU GLU ILE LEU LEU GLN LYS TRP GLU ASN GLY GLU SEQRES 6 A 162 CYS ALA GLN LYS LYS ILE ILE ALA GLU LYS THR LYS ILE SEQRES 7 A 162 PRO ALA VAL PHE LYS ILE ASP ALA LEU ASN GLU ASN LYS SEQRES 8 A 162 VAL LEU VAL LEU ASP THR ASP TYR LYS LYS TYR LEU LEU SEQRES 9 A 162 PHE CYS MET GLU ASN SER ALA GLU PRO GLU GLN SER LEU SEQRES 10 A 162 ALA CYS GLN CYS LEU VAL ARG THR PRO GLU VAL ASP ASP SEQRES 11 A 162 GLU ALA LEU GLU LYS PHE ASP LYS ALA LEU LYS ALA LEU SEQRES 12 A 162 PRO MET HIS ILE ARG LEU SER PHE ASN PRO THR GLN LEU SEQRES 13 A 162 GLU GLU GLN CYS HIS ILE HET VD3 A 163 28 HET VD3 A 164 28 HETNAM VD3 (1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6- HETNAM 2 VD3 METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4- HETNAM 3 VD3 YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL HETSYN VD3 VITAMIN D3 FORMUL 2 VD3 2(C27 H44 O) FORMUL 4 HOH *38(H2 O) HELIX 1 1 ASP A 11 ALA A 16 5 6 HELIX 2 2 ASP A 28 ASP A 33 1 6 HELIX 3 3 ASP A 129 ALA A 142 1 14 HELIX 4 4 ASN A 152 GLU A 157 1 6 HELIX 5 5 GLU A 158 ILE A 162 5 5 SHEET 1 A10 GLY A 17 THR A 18 0 SHEET 2 A10 VAL A 41 PRO A 48 -1 O LEU A 46 N GLY A 17 SHEET 3 A10 LEU A 54 GLU A 62 -1 O GLU A 55 N LYS A 47 SHEET 4 A10 GLU A 65 LYS A 75 -1 O ILE A 71 N ILE A 56 SHEET 5 A10 VAL A 81 ASP A 85 -1 O LYS A 83 N GLU A 74 SHEET 6 A10 GLU A 89 THR A 97 -1 O VAL A 92 N PHE A 82 SHEET 7 A10 TYR A 102 ASN A 109 -1 O LEU A 104 N ASP A 96 SHEET 8 A10 LEU A 117 VAL A 123 -1 O ALA A 118 N MET A 107 SHEET 9 A10 TYR A 20 ALA A 26 -1 N TYR A 20 O VAL A 123 SHEET 10 A10 ILE A 147 SER A 150 -1 O LEU A 149 N MET A 24 SSBOND 1 CYS A 66 CYS A 160 1555 1555 2.03 SSBOND 2 CYS A 106 CYS A 119 1555 1555 2.04 CISPEP 1 GLU A 112 PRO A 113 0 -0.14 SITE 1 AC1 12 PRO A 38 LEU A 39 VAL A 43 ILE A 56 SITE 2 AC1 12 LYS A 60 GLU A 62 ILE A 71 ILE A 84 SITE 3 AC1 12 ALA A 86 LEU A 87 PHE A 105 MET A 107 SITE 1 AC2 13 GLU A 134 ASP A 137 LYS A 138 LEU A 140 SITE 2 AC2 13 LYS A 141 LEU A 143 MET A 145 HIS A 146 SITE 3 AC2 13 ILE A 147 ARG A 148 LEU A 149 SER A 150 SITE 4 AC2 13 HOH A 194 CRYST1 53.782 53.782 111.578 90.00 90.00 120.00 P 32 2 1 6 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 0.018594 0.010735 0.000000 0.00000 SCALE2 0.000000 0.021470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008962 0.00000 MASTER 280 0 2 5 10 0 7 6 0 0 0 13 END