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 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 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