HEADER TRANSFERASE 30-APR-17 5XJ6 TITLE CRYSTAL STRUCTURE OF PLSY (YGIH), AN INTEGRAL MEMBRANE GLYCEROL 3- TITLE 2 PHOSPHATE ACYLTRANSFERASE - THE GLYCEROL 3-PHOSPHATE FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACYL-PO4 G3P ACYLTRANSFERASE,ACYL-PHOSPHATE--GLYCEROL-3- COMPND 5 PHOSPHATE ACYLTRANSFERASE,G3P ACYLTRANSFERASE,GPAT,LYSOPHOSPHATIDIC COMPND 6 ACID SYNTHASE,LPA SYNTHASE; COMPND 7 EC: 2.3.1.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: PLSY, AQ_676; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS GLYCEROL 3-PHOSPHATE ACYLTRANSFERASE, GLYCERYLPHOSPHATE KEYWDS 2 ACYLTRANSFERASE, GPAT, IN MESO, LIPID CUBIC PHASE, LIPIDIC CUBIC KEYWDS 3 PHASE, LIPID METABOLISM, MONOACYLGLYCEROL, PHOSPHOLIPID KEYWDS 4 BIOSYNTHESIS, PLSY, SUBSTRATE, YGIH, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.LI,Y.TANG,D.LI REVDAT 3 06-NOV-24 5XJ6 1 REMARK REVDAT 2 27-MAR-24 5XJ6 1 REMARK REVDAT 1 06-DEC-17 5XJ6 0 JRNL AUTH Z.LI,Y.TANG,Y.WU,S.ZHAO,J.BAO,Y.LUO,D.LI JRNL TITL STRUCTURAL INSIGHTS INTO THE COMMITTED STEP OF BACTERIAL JRNL TITL 2 PHOSPHOLIPID BIOSYNTHESIS. JRNL REF NAT COMMUN V. 8 1691 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29167463 JRNL DOI 10.1038/S41467-017-01821-9 REMARK 2 REMARK 2 RESOLUTION. 2.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 8438 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.240 REMARK 3 FREE R VALUE TEST SET COUNT : 442 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 45.8482 - 3.4171 0.99 2792 146 0.2116 0.2389 REMARK 3 2 3.4171 - 2.7124 1.00 2656 158 0.2335 0.3102 REMARK 3 3 2.7124 - 2.3695 0.97 2548 138 0.2210 0.2796 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.320 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 : 0.003 1712 REMARK 3 ANGLE : 0.626 2300 REMARK 3 CHIRALITY : 0.037 264 REMARK 3 PLANARITY : 0.003 272 REMARK 3 DIHEDRAL : 10.347 1306 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5XJ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1300003348. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8548 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 45.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 1.14500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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 (%): 45.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35-38% PEG 400, 0.1-0.2M LICL, 0.1M REMARK 280 TRIS HCL PH 8.0, 80MM GLYCEROL PHOSPHATE, LIPIDIC CUBIC PHASE, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.88600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.84400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.88600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.84400 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 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 FME A 0 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue G3P A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XJ5 RELATED DB: PDB REMARK 900 RELATED ID: 5XJ7 RELATED DB: PDB REMARK 900 RELATED ID: 5XJ8 RELATED DB: PDB REMARK 900 RELATED ID: 5XJ9 RELATED DB: PDB DBREF 5XJ6 A 3 192 UNP O66905 PLSY_AQUAE 3 192 SEQADV 5XJ6 FME A 0 UNP O66905 EXPRESSION TAG SEQADV 5XJ6 GLY A 1 UNP O66905 EXPRESSION TAG SEQADV 5XJ6 SER A 2 UNP O66905 EXPRESSION TAG SEQADV 5XJ6 GLY A 193 UNP O66905 EXPRESSION TAG SEQADV 5XJ6 THR A 194 UNP O66905 EXPRESSION TAG SEQADV 5XJ6 LEU A 195 UNP O66905 EXPRESSION TAG SEQADV 5XJ6 GLU A 196 UNP O66905 EXPRESSION TAG SEQADV 5XJ6 VAL A 197 UNP O66905 EXPRESSION TAG SEQADV 5XJ6 LEU A 198 UNP O66905 EXPRESSION TAG SEQADV 5XJ6 PHE A 199 UNP O66905 EXPRESSION TAG SEQADV 5XJ6 GLN A 200 UNP O66905 EXPRESSION TAG SEQRES 1 A 201 FME GLY SER ALA LEU PHE LEU VAL ILE PHE ALA TYR LEU SEQRES 2 A 201 LEU GLY SER ILE THR PHE GLY GLU VAL ILE ALA LYS LEU SEQRES 3 A 201 LYS GLY VAL ASP LEU ARG ASN VAL GLY SER GLY ASN VAL SEQRES 4 A 201 GLY ALA THR ASN VAL THR ARG ALA LEU GLY LYS LYS TYR SEQRES 5 A 201 GLY VAL LEU VAL PHE PHE LEU ASP PHE LEU LYS GLY PHE SEQRES 6 A 201 ILE PRO ALA LEU ILE ALA VAL LYS SER PHE GLY ILE ASP SEQRES 7 A 201 SER TRP VAL LEU THR PHE THR GLY LEU ALA SER VAL LEU SEQRES 8 A 201 GLY HIS MET TYR PRO VAL PHE PHE GLY PHE LYS GLY GLY SEQRES 9 A 201 LYS GLY VAL ALA THR ALA LEU GLY VAL VAL PHE ALA VAL SEQRES 10 A 201 SER PRO SER VAL ALA LEU PHE SER PHE LEU VAL TRP LEU SEQRES 11 A 201 GLY ILE PHE LEU TRP LYS ARG TYR VAL SER LEU ALA SER SEQRES 12 A 201 ILE THR ALA THR ILE SER ALA PHE LEU PHE LEU PHE VAL SEQRES 13 A 201 ALA GLY TYR PRO VAL ASN VAL LEU PHE MET ALA ILE VAL SEQRES 14 A 201 ILE GLY ALA LEU ILE ILE TYR ARG HIS ARG GLU ASN ILE SEQRES 15 A 201 ASN ARG LEU LEU THR GLY ARG GLU HIS ARG PHE GLY THR SEQRES 16 A 201 LEU GLU VAL LEU PHE GLN HET G3P A 301 10 HET OLC A 302 25 HET OLC A 303 25 HET OLC A 304 25 HET OLC A 305 25 HET PO4 A 306 5 HETNAM G3P SN-GLYCEROL-3-PHOSPHATE HETNAM OLC (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE HETNAM PO4 PHOSPHATE ION HETSYN OLC 1-OLEOYL-R-GLYCEROL FORMUL 2 G3P C3 H9 O6 P FORMUL 3 OLC 4(C21 H40 O4) FORMUL 7 PO4 O4 P 3- FORMUL 8 HOH *16(H2 O) HELIX 1 AA1 GLY A 1 SER A 15 1 15 HELIX 2 AA2 THR A 17 GLY A 27 1 11 HELIX 3 AA3 GLY A 39 GLY A 48 1 10 HELIX 4 AA4 GLY A 48 GLY A 75 1 28 HELIX 5 AA5 SER A 78 TYR A 94 1 17 HELIX 6 AA6 GLY A 105 SER A 117 1 13 HELIX 7 AA7 SER A 117 ARG A 136 1 20 HELIX 8 AA8 TYR A 137 ALA A 156 1 20 HELIX 9 AA9 PRO A 159 HIS A 177 1 19 HELIX 10 AB1 HIS A 177 THR A 186 1 10 HELIX 11 AB2 GLY A 193 GLN A 200 1 8 SITE 1 AC1 11 SER A 35 THR A 41 ARG A 45 LYS A 104 SITE 2 AC1 11 VAL A 138 SER A 142 HIS A 177 ASN A 180 SITE 3 AC1 11 PO4 A 306 HOH A 401 HOH A 403 SITE 1 AC2 9 PHE A 56 LEU A 110 TRP A 128 PHE A 132 SITE 2 AC2 9 ALA A 145 ALA A 166 VAL A 197 LEU A 198 SITE 3 AC2 9 GLN A 200 SITE 1 AC3 5 PHE A 83 ILE A 131 TRP A 134 PHE A 152 SITE 2 AC3 5 VAL A 168 SITE 1 AC4 5 SER A 119 LEU A 122 TYR A 175 ARG A 178 SITE 2 AC4 5 OLC A 305 SITE 1 AC5 11 TYR A 11 TYR A 94 PHE A 100 SER A 117 SITE 2 AC5 11 SER A 119 VAL A 120 PHE A 152 ALA A 156 SITE 3 AC5 11 TYR A 158 TYR A 175 OLC A 304 SITE 1 AC6 8 ASN A 37 GLY A 39 HIS A 92 GLY A 103 SITE 2 AC6 8 LYS A 104 GLY A 105 VAL A 106 G3P A 301 CRYST1 42.148 53.772 87.688 90.00 90.00 90.00 P 2 21 21 4 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 0.023726 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018597 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011404 0.00000