HEADER LIPID BINDING PROTEIN 14-OCT-16 5H28
TITLE CRYSTAL STRUCTURE OF OSH1 ANK DOMAIN FROM SACCHAROMYCES CEREVISIA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: OXYSTEROL-BINDING PROTEIN HOMOLOG 1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 12-274;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 /
SOURCE 3 S288C);
SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE 5 ORGANISM_TAXID: 559292;
SOURCE 6 STRAIN: ATCC 204508 / S288C;
SOURCE 7 GENE: SWH1, OSH1, YAR042W, YAR044W;
SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 12 EXPRESSION_SYSTEM_PLASMID: MODIFIED PHIS-2
KEYWDS OXYSTEROL BINDING, LIPID TRANSFER, ANK NVJ1, LIPID BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.J.IM,M.K.MANIK,H.S.YANG,J.S.TONG
REVDAT 2 20-MAR-24 5H28 1 REMARK
REVDAT 1 17-MAY-17 5H28 0
JRNL AUTH M.K.MANIK,H.YANG,J.TONG,Y.J.IM
JRNL TITL STRUCTURE OF YEAST OSBP-RELATED PROTEIN OSH1 REVEALS KEY
JRNL TITL 2 DETERMINANTS FOR LIPID TRANSPORT AND PROTEIN TARGETING AT
JRNL TITL 3 THE NUCLEUS-VACUOLE JUNCTION
JRNL REF STRUCTURE V. 25 617 2017
JRNL REFN ISSN 1878-4186
JRNL PMID 28319008
JRNL DOI 10.1016/J.STR.2017.02.010
REMARK 2
REMARK 2 RESOLUTION. 1.50 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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.55
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 693450.380
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6
REMARK 3 NUMBER OF REFLECTIONS : 32045
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) : 0.184
REMARK 3 FREE R VALUE : 0.214
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1588
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.10
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4912
REMARK 3 BIN R VALUE (WORKING SET) : 0.2020
REMARK 3 BIN FREE R VALUE : 0.2410
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 247
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2107
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 315
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 13.90
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.30
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.08000
REMARK 3 B22 (A**2) : -2.76000
REMARK 3 B33 (A**2) : 2.68000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 1.11000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15
REMARK 3 ESD FROM SIGMAA (A) : 0.08
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) : 0.18
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.004
REMARK 3 BOND ANGLES (DEGREES) : 1.200
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.10
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870
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 : 0.38
REMARK 3 BSOL : 52.48
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 : CNS_TOPPAR/PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR/WATER_REP.PARAM
REMARK 3 PARAMETER FILE 3 : NULL
REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR/PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : CNS_TOPPAR/WATER.TOP
REMARK 3 TOPOLOGY FILE 3 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5H28 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-OCT-16.
REMARK 100 THE DEPOSITION ID IS D_1300001877.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-JUL-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PAL/PLS
REMARK 200 BEAMLINE : 7A (6B, 6C1)
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950
REMARK 200 MONOCHROMATOR : SI CRYSTAL
REMARK 200 OPTICS : FOCUSING MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80061
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 200 DATA REDUNDANCY : 4.100
REMARK 200 R MERGE (I) : 0.06200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0
REMARK 200 DATA REDUNDANCY IN SHELL : 4.10
REMARK 200 R MERGE FOR SHELL (I) : 0.37100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 28.97
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NAOH PH 7.0, 20% PEG 1500,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 36.10100
REMARK 290 SMTRY3 2 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 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 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 SER A 269 -48.09 71.75
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5H2A RELATED DB: PDB
REMARK 900 RELATED ID: 5H2C RELATED DB: PDB
REMARK 900 RELATED ID: 5H2D RELATED DB: PDB
DBREF 5H28 A 12 274 UNP P35845 OSH1_YEAST 12 274
SEQRES 1 A 263 SER LYS PRO LEU LEU LYS LEU LYS LEU LEU ASP ALA LEU
SEQRES 2 A 263 ARG GLN GLY SER PHE PRO ASN LEU GLN ASP LEU LEU LYS
SEQRES 3 A 263 LYS GLN PHE GLN PRO LEU ASP ASP PRO ASN VAL GLN GLN
SEQRES 4 A 263 VAL LEU HIS LEU MET LEU HIS TYR ALA VAL GLN VAL ALA
SEQRES 5 A 263 PRO MET ALA VAL ILE LYS GLU ILE VAL HIS HIS TRP VAL
SEQRES 6 A 263 SER THR THR ASN THR THR PHE LEU ASN ILE HIS LEU ASP
SEQRES 7 A 263 LEU ASN GLU ARG ASP SER ASN GLY ASN THR PRO LEU HIS
SEQRES 8 A 263 ILE ALA ALA TYR GLN SER ARG GLY ASP ILE VAL ALA PHE
SEQRES 9 A 263 LEU LEU ASP GLN PRO THR ILE ASN ASP CYS VAL LEU ASN
SEQRES 10 A 263 ASN SER HIS LEU GLN ALA ILE GLU MET CYS LYS ASN LEU
SEQRES 11 A 263 ASN ILE ALA GLN MET MET GLN VAL LYS ARG SER THR TYR
SEQRES 12 A 263 VAL ALA GLU THR ALA GLN GLU PHE ARG THR ALA PHE ASN
SEQRES 13 A 263 ASN ARG ASP PHE GLY HIS LEU GLU SER ILE LEU SER SER
SEQRES 14 A 263 PRO ARG ASN ALA GLU LEU LEU ASP ILE ASN GLY MET ASP
SEQRES 15 A 263 PRO GLU THR GLY ASP THR VAL LEU HIS GLU PHE VAL LYS
SEQRES 16 A 263 LYS ARG ASP VAL ILE MET CYS ARG TRP LEU LEU GLU HIS
SEQRES 17 A 263 GLY ALA ASP PRO PHE LYS ARG ASP ARG LYS GLY LYS LEU
SEQRES 18 A 263 PRO ILE GLU LEU VAL ARG LYS VAL ASN GLU ASN ASP THR
SEQRES 19 A 263 ALA THR ASN THR LYS ILE ALA ILE ASP ILE GLU LEU LYS
SEQRES 20 A 263 LYS LEU LEU GLU ARG ALA THR ARG GLU GLN SER VAL ILE
SEQRES 21 A 263 ASP VAL THR
FORMUL 2 HOH *315(H2 O)
HELIX 1 AA1 SER A 12 GLY A 27 1 16
HELIX 2 AA2 SER A 28 PHE A 40 1 13
HELIX 3 AA3 ASP A 45 LEU A 54 1 10
HELIX 4 AA4 LEU A 54 ALA A 63 1 10
HELIX 5 AA5 PRO A 64 VAL A 76 1 13
HELIX 6 AA6 THR A 99 GLN A 107 1 9
HELIX 7 AA7 ARG A 109 ASP A 118 1 10
HELIX 8 AA8 GLN A 133 CYS A 138 5 6
HELIX 9 AA9 ASN A 140 ASN A 168 1 29
HELIX 10 AB1 ASP A 170 SER A 179 1 10
HELIX 11 AB2 ARG A 182 LEU A 187 1 6
HELIX 12 AB3 THR A 199 ARG A 208 1 10
HELIX 13 AB4 ASP A 209 HIS A 219 1 11
HELIX 14 AB5 LEU A 232 VAL A 237 5 6
HELIX 15 AB6 ASN A 248 LYS A 250 5 3
HELIX 16 AB7 ILE A 251 GLN A 268 1 18
CISPEP 1 GLN A 41 PRO A 42 0 -0.44
CRYST1 29.465 72.202 49.008 90.00 93.53 90.00 P 1 21 1 2
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 0.033939 0.000000 0.002095 0.00000
SCALE2 0.000000 0.013850 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020444 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
