HEADER PHOSPHOLIPID-BINDING PROTEIN 20-AUG-97 1AUA TITLE PHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P FROM SACCHAROMYCES TITLE 2 CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: SEC14; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: KK2186; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE-31; SOURCE 10 EXPRESSION_SYSTEM_GENE: SEC14 KEYWDS PHOSPHOLIPID-BINDING PROTEIN, PERIPHERAL GOLGI MEMBRANE PROTEIN, KEYWDS 2 PHOSPHOLIPID EXCHANGE, GOLGI-DERIVED SECRETORY VESICLE BIOGENESIS EXPDTA X-RAY DIFFRACTION AUTHOR B.SHA,S.E.PHILLIPS,V.A.BANKAITIS,M.LUO REVDAT 4 07-FEB-24 1AUA 1 HETSYN REVDAT 3 29-JUL-20 1AUA 1 COMPND REMARK HETNAM SITE REVDAT 2 24-FEB-09 1AUA 1 VERSN REVDAT 1 24-DEC-97 1AUA 0 JRNL AUTH B.SHA,S.E.PHILLIPS,V.A.BANKAITIS,M.LUO JRNL TITL CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE JRNL TITL 2 PHOSPHATIDYLINOSITOL-TRANSFER PROTEIN. JRNL REF NATURE V. 391 506 1998 JRNL REFN ISSN 0028-0836 JRNL PMID 9461221 JRNL DOI 10.1038/35179 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.85 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 16259 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) : 0.211 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1083 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.61 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2029 REMARK 3 BIN R VALUE (WORKING SET) : 0.3540 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 64 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.039 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2400 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.24 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) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 30.0 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.422 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.08 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.218 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM3.CHO REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH3.CHO REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE PARAMETER AND TOPOLOGY FILES ARE REMARK 3 AVAILABLE FROM DR. B.SHA. REMARK 4 REMARK 4 1AUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171266. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL 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 : 16736 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3% PEG 3350, 1% N-OCTYL B-D REMARK 280 -GLUCOPYRANOSIDE, 10 MM HEPES, 150MM KCL, PH 7.2 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 74.22600 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 37.11300 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 37.11300 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 74.22600 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: DIMERIC 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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLN A 5 -55.58 -130.98 REMARK 500 ASP A 30 -53.26 -153.53 REMARK 500 SER A 31 78.54 -53.58 REMARK 500 ALA A 32 -16.75 59.81 REMARK 500 GLU A 39 -45.86 -171.33 REMARK 500 LYS A 66 19.19 48.57 REMARK 500 TYR A 107 77.31 -166.45 REMARK 500 PRO A 108 -84.29 -26.87 REMARK 500 GLN A 109 107.40 55.45 REMARK 500 LYS A 113 -154.77 48.74 REMARK 500 THR A 138 -158.31 -111.04 REMARK 500 LEU A 169 -92.78 -45.96 REMARK 500 VAL A 170 95.35 84.98 REMARK 500 TYR A 205 51.64 -146.23 REMARK 500 PRO A 256 -93.39 -25.91 REMARK 500 ALA A 257 -38.70 168.34 REMARK 500 LYS A 274 36.03 -156.75 REMARK 500 LEU A 277 -69.73 67.36 REMARK 500 ASP A 281 63.31 -151.29 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AUA A 4 299 UNP P24280 SEC14_YEAST 3 298 SEQRES 1 A 296 GLN GLN GLU LYS GLU PHE LEU GLU SER TYR PRO GLN ASN SEQRES 2 A 296 CYS PRO PRO ASP ALA LEU PRO GLY THR PRO GLY ASN LEU SEQRES 3 A 296 ASP SER ALA GLN GLU LYS ALA LEU ALA GLU LEU ARG LYS SEQRES 4 A 296 LEU LEU GLU ASP ALA GLY PHE ILE GLU ARG LEU ASP ASP SEQRES 5 A 296 SER THR LEU LEU ARG PHE LEU ARG ALA ARG LYS PHE ASP SEQRES 6 A 296 VAL GLN LEU ALA LYS GLU MET PHE GLU ASN CYS GLU LYS SEQRES 7 A 296 TRP ARG LYS ASP TYR GLY THR ASP THR ILE LEU GLN ASP SEQRES 8 A 296 PHE HIS TYR ASP GLU LYS PRO LEU ILE ALA LYS PHE TYR SEQRES 9 A 296 PRO GLN TYR TYR HIS LYS THR ASP LYS ASP GLY ARG PRO SEQRES 10 A 296 VAL TYR PHE GLU GLU LEU GLY ALA VAL ASN LEU HIS GLU SEQRES 11 A 296 MET ASN LYS VAL THR SER GLU GLU ARG MET LEU LYS ASN SEQRES 12 A 296 LEU VAL TRP GLU TYR GLU SER VAL VAL GLN TYR ARG LEU SEQRES 13 A 296 PRO ALA CYS SER ARG ALA ALA GLY HIS LEU VAL GLU THR SEQRES 14 A 296 SER CYS THR ILE MET ASP LEU LYS GLY ILE SER ILE SER SEQRES 15 A 296 SER ALA TYR SER VAL MET SER TYR VAL ARG GLU ALA SER SEQRES 16 A 296 TYR ILE SER GLN ASN TYR TYR PRO GLU ARG MET GLY LYS SEQRES 17 A 296 PHE TYR ILE ILE ASN ALA PRO PHE GLY PHE SER THR ALA SEQRES 18 A 296 PHE ARG LEU PHE LYS PRO PHE LEU ASP PRO VAL THR VAL SEQRES 19 A 296 SER LYS ILE PHE ILE LEU GLY SER SER TYR GLN LYS GLU SEQRES 20 A 296 LEU LEU LYS GLN ILE PRO ALA GLU ASN LEU PRO VAL LYS SEQRES 21 A 296 PHE GLY GLY LYS SER GLU VAL ASP GLU SER LYS GLY GLY SEQRES 22 A 296 LEU TYR LEU SER ASP ILE GLY PRO TRP ARG ASP PRO LYS SEQRES 23 A 296 TYR ILE GLY PRO GLU GLY GLU ALA PRO GLU HET BOG A 1 20 HET BOG A 2 20 HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D- HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE FORMUL 2 BOG 2(C14 H28 O6) FORMUL 4 HOH *53(H2 O) HELIX 1 1 GLU A 6 SER A 12 1 7 HELIX 2 2 GLN A 33 ASP A 46 1 14 HELIX 3 3 ASP A 55 ALA A 64 1 10 HELIX 4 4 VAL A 69 TYR A 86 1 18 HELIX 5 5 THR A 88 ASP A 94 5 7 HELIX 6 6 LYS A 100 PHE A 106 1 7 HELIX 7 7 LEU A 126 ALA A 128 5 3 HELIX 8 8 LEU A 131 MET A 134 1 4 HELIX 9 9 GLU A 140 GLN A 156 1 17 HELIX 10 10 ARG A 158 ALA A 166 1 9 HELIX 11 11 ILE A 184 TYR A 204 1 21 HELIX 12 12 PHE A 219 PHE A 231 1 13 HELIX 13 13 PRO A 234 VAL A 237 1 4 HELIX 14 14 GLN A 248 LEU A 251 1 4 HELIX 15 15 VAL A 262 PHE A 264 5 3 HELIX 16 16 GLU A 272 LYS A 274 5 3 HELIX 17 17 PRO A 284 ARG A 286 5 3 HELIX 18 18 PRO A 288 TYR A 290 5 3 SHEET 1 A 4 PRO A 120 GLU A 124 0 SHEET 2 A 4 SER A 173 ASP A 178 1 N CYS A 174 O PRO A 120 SHEET 3 A 4 MET A 209 ILE A 215 1 N GLY A 210 O SER A 173 SHEET 4 A 4 ILE A 240 ILE A 242 1 N PHE A 241 O PHE A 212 CRYST1 88.971 88.971 111.339 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 0.011240 0.006489 0.000000 0.00000 SCALE2 0.000000 0.012978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008982 0.00000