HEADER LIPID BINDING PROTEIN 03-APR-22 7ZGA TITLE STRUCTURE OF YEAST SEC14P WITH ERGOLINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEC14 CYTOSOLIC FACTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHATIDYLINOSITOL/PHOSPHATIDYLCHOLINE TRANSFER PROTEIN, COMPND 5 PI/PC TP; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_TAXID: 559292; SOURCE 4 STRAIN: ATCC 204508 / S288C; SOURCE 5 GENE: SEC14, PIT1, YMR079W, YM9582.04; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SEC14P, ERGOLINE, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.HONG,P.JOHNEN,G.SCHAAF,F.BONO REVDAT 3 07-FEB-24 7ZGA 1 REMARK REVDAT 2 08-FEB-23 7ZGA 1 JRNL REVDAT 1 25-JAN-23 7ZGA 0 JRNL AUTH X.R.CHEN,L.POUDEL,Z.HONG,P.JOHNEN,S.KATTI,A.TRIPATHI, JRNL AUTH 2 A.H.NILE,S.M.GREEN,D.KHAN,G.SCHAAF,F.BONO,V.A.BANKAITIS, JRNL AUTH 3 T.I.IGUMENOVA JRNL TITL MECHANISMS BY WHICH SMALL MOLECULES OF DIVERSE CHEMOTYPES JRNL TITL 2 ARREST SEC14 LIPID TRANSFER ACTIVITY. JRNL REF J.BIOL.CHEM. V. 299 02861 2023 JRNL REFN ESSN 1083-351X JRNL PMID 36603766 JRNL DOI 10.1016/J.JBC.2022.102861 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 22066 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2007 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.5290 - 5.5437 1.00 1547 157 0.1880 0.2090 REMARK 3 2 5.5437 - 4.4014 1.00 1466 147 0.1629 0.2240 REMARK 3 3 4.4014 - 3.8454 1.00 1447 148 0.1615 0.1721 REMARK 3 4 3.8454 - 3.4940 1.00 1444 142 0.1764 0.2149 REMARK 3 5 3.4940 - 3.2436 1.00 1429 141 0.1991 0.2332 REMARK 3 6 3.2436 - 3.0524 1.00 1432 144 0.2094 0.2783 REMARK 3 7 3.0524 - 2.8996 1.00 1432 143 0.1945 0.2578 REMARK 3 8 2.8996 - 2.7734 1.00 1437 143 0.2035 0.2773 REMARK 3 9 2.7734 - 2.6666 1.00 1413 137 0.2010 0.2456 REMARK 3 10 2.6666 - 2.5746 1.00 1397 141 0.2028 0.2581 REMARK 3 11 2.5746 - 2.4941 1.00 1409 143 0.2257 0.2630 REMARK 3 12 2.4941 - 2.4229 1.00 1431 141 0.2212 0.2981 REMARK 3 13 2.4229 - 2.3591 1.00 1421 144 0.2411 0.2507 REMARK 3 14 2.3591 - 2.3020 0.97 1354 136 0.2687 0.3258 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.700 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2422 REMARK 3 ANGLE : 1.021 3297 REMARK 3 CHIRALITY : 0.055 350 REMARK 3 PLANARITY : 0.006 432 REMARK 3 DIHEDRAL : 13.665 1450 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 17.8216 101.2479 1.2943 REMARK 3 T TENSOR REMARK 3 T11: 0.2993 T22: 0.3253 REMARK 3 T33: 0.2962 T12: -0.0348 REMARK 3 T13: -0.0046 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 0.7564 L22: 1.6321 REMARK 3 L33: 0.7604 L12: 0.2716 REMARK 3 L13: -0.5256 L23: -0.4659 REMARK 3 S TENSOR REMARK 3 S11: -0.0358 S12: 0.0148 S13: -0.0279 REMARK 3 S21: 0.1324 S22: 0.0458 S23: -0.0597 REMARK 3 S31: -0.0080 S32: -0.0135 S33: 0.0001 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7ZGA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-22. REMARK 100 THE DEPOSITION ID IS D_1292122208. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 124 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41643 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 44.529 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 6.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: PHASER REMARK 200 STARTING MODEL: 1AUA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 129,5 MM SODIUM ACETATE, 64,8 MM TRIS, REMARK 280 4,6 % (W/V) PEG 4000, AND 11.9 % (V/V) GLYCEROL ADJUSTED TO PH REMARK 280 7.0, EVAPORATION, TEMPERATURE 294K 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 73.37867 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 36.68933 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 36.68933 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 73.37867 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG A 63 O HOH A 401 1.97 REMARK 500 O HOH A 474 O HOH A 475 2.03 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 TYR A 107 70.51 -163.85 REMARK 500 LYS A 113 -158.65 60.74 REMARK 500 TYR A 157 -52.44 -123.95 REMARK 500 ASP A 233 130.41 -37.58 REMARK 500 ASP A 281 68.34 -151.81 REMARK 500 REMARK 500 REMARK: NULL DBREF 7ZGA A 3 298 UNP P24280 SEC14_YEAST 3 298 SEQRES 1 A 296 THR GLN GLN GLU LYS GLU PHE LEU GLU SER TYR PRO GLN SEQRES 2 A 296 ASN CYS PRO PRO ASP ALA LEU PRO GLY THR PRO GLY ASN SEQRES 3 A 296 LEU ASP SER ALA GLN GLU LYS ALA LEU ALA GLU LEU ARG SEQRES 4 A 296 LYS LEU LEU GLU ASP ALA GLY PHE ILE GLU ARG LEU ASP SEQRES 5 A 296 ASP SER THR LEU LEU ARG PHE LEU ARG ALA ARG LYS PHE SEQRES 6 A 296 ASP VAL GLN LEU ALA LYS GLU MET PHE GLU ASN CYS GLU SEQRES 7 A 296 LYS TRP ARG LYS ASP TYR GLY THR ASP THR ILE LEU GLN SEQRES 8 A 296 ASP PHE HIS TYR ASP GLU LYS PRO LEU ILE ALA LYS PHE SEQRES 9 A 296 TYR PRO GLN TYR TYR HIS LYS THR ASP LYS ASP GLY ARG SEQRES 10 A 296 PRO VAL TYR PHE GLU GLU LEU GLY ALA VAL ASN LEU HIS SEQRES 11 A 296 GLU MET ASN LYS VAL THR SER GLU GLU ARG MET LEU LYS SEQRES 12 A 296 ASN LEU VAL TRP GLU TYR GLU SER VAL VAL GLN TYR ARG SEQRES 13 A 296 LEU PRO ALA CYS SER ARG ALA ALA GLY HIS LEU VAL GLU SEQRES 14 A 296 THR SER CYS THR ILE MET ASP LEU LYS GLY ILE SER ILE SEQRES 15 A 296 SER SER ALA TYR SER VAL MET SER TYR VAL ARG GLU ALA SEQRES 16 A 296 SER TYR ILE SER GLN ASN TYR TYR PRO GLU ARG MET GLY SEQRES 17 A 296 LYS PHE TYR ILE ILE ASN ALA PRO PHE GLY PHE SER THR SEQRES 18 A 296 ALA PHE ARG LEU PHE LYS PRO PHE LEU ASP PRO VAL THR SEQRES 19 A 296 VAL SER LYS ILE PHE ILE LEU GLY SER SER TYR GLN LYS SEQRES 20 A 296 GLU LEU LEU LYS GLN ILE PRO ALA GLU ASN LEU PRO VAL SEQRES 21 A 296 LYS PHE GLY GLY LYS SER GLU VAL ASP GLU SER LYS GLY SEQRES 22 A 296 GLY LEU TYR LEU SER ASP ILE GLY PRO TRP ARG ASP PRO SEQRES 23 A 296 LYS TYR ILE GLY PRO GLU GLY GLU ALA PRO HET IUF A 301 32 HETNAM IUF ~{O}9-METHYL ~{O}4-[2,2,2-TRIS(CHLORANYL)ETHYL] HETNAM 2 IUF (5~{A}~{S},6~{A}~{S},9~{R},10~{A}~{S})-7-METHYL-3- HETNAM 3 IUF NITRO-5,5~{A},6,6~{A},8,9,10,10~{A}-OCTAHYDROINDOLO[4, HETNAM 4 IUF 3-FG]QUINOLINE-4,9-DICARBOXYLATE FORMUL 2 IUF C20 H22 CL3 N3 O6 FORMUL 3 HOH *77(H2 O) HELIX 1 AA1 THR A 3 GLU A 11 1 9 HELIX 2 AA2 ASP A 30 ALA A 47 1 18 HELIX 3 AA3 ASP A 54 ARG A 65 1 12 HELIX 4 AA4 ASP A 68 GLY A 87 1 20 HELIX 5 AA5 THR A 90 PHE A 95 1 6 HELIX 6 AA6 GLU A 99 ALA A 104 1 6 HELIX 7 AA7 LYS A 105 TYR A 107 5 3 HELIX 8 AA8 LEU A 126 VAL A 129 5 4 HELIX 9 AA9 ASN A 130 ASN A 135 1 6 HELIX 10 AB1 SER A 139 TYR A 157 1 19 HELIX 11 AB2 TYR A 157 GLY A 167 1 11 HELIX 12 AB3 SER A 183 TYR A 205 1 23 HELIX 13 AB4 PRO A 218 LYS A 229 1 12 HELIX 14 AB5 PRO A 230 LEU A 232 5 3 HELIX 15 AB6 ASP A 233 LYS A 239 1 7 HELIX 16 AB7 TYR A 247 ILE A 255 1 9 HELIX 17 AB8 PRO A 261 GLY A 265 5 5 HELIX 18 AB9 ASP A 271 GLY A 275 5 5 HELIX 19 AC1 GLY A 276 SER A 280 5 5 HELIX 20 AC2 GLY A 283 ILE A 291 5 9 SHEET 1 AA1 5 GLN A 109 THR A 114 0 SHEET 2 AA1 5 PRO A 120 GLU A 124 -1 O PHE A 123 N TYR A 110 SHEET 3 AA1 5 SER A 173 ASP A 178 1 O CYS A 174 N TYR A 122 SHEET 4 AA1 5 MET A 209 ILE A 215 1 O TYR A 213 N THR A 175 SHEET 5 AA1 5 ILE A 240 ILE A 242 1 O PHE A 241 N ILE A 214 CRYST1 87.498 87.498 110.068 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 0.011429 0.006598 0.000000 0.00000 SCALE2 0.000000 0.013197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009085 0.00000