HEADER IMMUNE SYSTEM 26-JUL-23 8PYV TITLE STRUCTURE OF HUMAN PS-1 GSH-ANALOG COMPLEX, SOLVED AT WAVELENGTH 2.755 TITLE 2 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROSTAGLANDIN E SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLUTATHIONE PEROXIDASE PTGES,GLUTATHIONE TRANSFERASE PTGES, COMPND 5 MICROSOMAL GLUTATHIONE S-TRANSFERASE 1-LIKE 1,MGST1-L1,MICROSOMAL COMPND 6 PROSTAGLANDIN E SYNTHASE 1,MPGES-1,P53-INDUCED GENE 12 PROTEIN; COMPND 7 EC: 5.3.99.3,1.11.1.-,2.5.1.18; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PTGES, MGST1L1, MPGES1, PGES, PIG12; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS MEMBRANE PROTEIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.DUMAN,K.EL OMARI,V.MYKHAYLYK,C.ORR,A.WAGNER,L.VOGELEY,D.G.BROWN REVDAT 1 25-OCT-23 8PYV 0 JRNL AUTH K.EL OMARI,R.DUMAN,V.MYKHAYLYK,C.M.ORR,M.LATIMER-SMITH, JRNL AUTH 2 G.WINTER,V.GRAMA,F.QU,K.BOUNTRA,H.S.KWONG,M.ROMANO,R.I.REIS, JRNL AUTH 3 L.VOGELEY,L.VECCHIA,C.D.OWEN,S.WITTMANN,M.RENNER,M.SENDA, JRNL AUTH 4 N.MATSUGAKI,Y.KAWANO,T.A.BOWDEN,I.MORAES,J.M.GRIMES, JRNL AUTH 5 E.J.MANCINI,M.A.WALSH,C.R.GUZZO,R.J.OWENS,E.Y.JONES, JRNL AUTH 6 D.G.BROWN,D.I.STUART,K.BEIS,A.WAGNER JRNL TITL EXPERIMENTAL PHASING OPPORTUNITIES FOR MACROMOLECULAR JRNL TITL 2 CRYSTALLOGRAPHY AT VERY LONG WAVELENGTHS. JRNL REF COMMUN CHEM V. 6 219 2023 JRNL REFN ESSN 2399-3669 JRNL PMID 37828292 JRNL DOI 10.1038/S42004-023-01014-0 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.580 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 25736 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1276 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 58.6400 - 3.6900 0.95 2791 143 0.1739 0.1783 REMARK 3 2 3.6800 - 2.9300 0.96 2817 119 0.1808 0.2246 REMARK 3 3 2.9200 - 2.5600 0.94 2767 164 0.1961 0.1950 REMARK 3 4 2.5500 - 2.3200 0.95 2764 160 0.2147 0.2261 REMARK 3 5 2.3200 - 2.1500 0.96 2796 118 0.2341 0.2323 REMARK 3 6 2.1500 - 2.0300 0.95 2796 149 0.2659 0.2610 REMARK 3 7 2.0300 - 1.9300 0.95 2801 147 0.3520 0.3628 REMARK 3 8 1.9300 - 1.8400 0.95 2767 139 0.5093 0.6124 REMARK 3 9 1.8400 - 1.7700 0.74 2181 117 0.6340 0.5304 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.04 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 : 0.011 1244 REMARK 3 ANGLE : 1.139 1682 REMARK 3 CHIRALITY : 0.053 187 REMARK 3 PLANARITY : 0.013 210 REMARK 3 DIHEDRAL : 16.899 185 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): 10.0137 -1.2561 49.5994 REMARK 3 T TENSOR REMARK 3 T11: 0.2582 T22: 0.2579 REMARK 3 T33: 0.2289 T12: 0.0038 REMARK 3 T13: 0.0006 T23: 0.0024 REMARK 3 L TENSOR REMARK 3 L11: 0.2675 L22: 0.3527 REMARK 3 L33: 0.3590 L12: -0.0404 REMARK 3 L13: 0.0150 L23: -0.1167 REMARK 3 S TENSOR REMARK 3 S11: 0.0268 S12: -0.0122 S13: 0.0022 REMARK 3 S21: -0.0071 S22: -0.0268 S23: -0.0475 REMARK 3 S31: 0.0301 S32: 0.0879 S33: -0.0029 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 8PYV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292132239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I23 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 2.7552 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 12M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26090 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 58.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 17.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 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: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS PH 8 , % PEG400, 100 MM REMARK 280 NACL AND 1MM TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.60000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.28572 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.68667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 38.60000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 22.28572 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.68667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 38.60000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 22.28572 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.68667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.57144 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 81.37333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 44.57144 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 81.37333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 44.57144 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 81.37333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL 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 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 324 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 PRO A 2 REMARK 465 ALA A 3 REMARK 465 HIS A 4 REMARK 465 SER A 5 REMARK 465 LEU A 6 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 O HOH A 311 O HOH A 332 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PLM A 201 REMARK 610 PLM A 202 REMARK 610 48T A 203 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 324 DBREF 8PYV A 1 152 UNP O14684 PTGES_HUMAN 1 152 SEQRES 1 A 152 MET PRO ALA HIS SER LEU VAL MET SER SER PRO ALA LEU SEQRES 2 A 152 PRO ALA PHE LEU LEU CYS SER THR LEU LEU VAL ILE LYS SEQRES 3 A 152 MET TYR VAL VAL ALA ILE ILE THR GLY GLN VAL ARG LEU SEQRES 4 A 152 ARG LYS LYS ALA PHE ALA ASN PRO GLU ASP ALA LEU ARG SEQRES 5 A 152 HIS GLY GLY PRO GLN TYR CYS ARG SER ASP PRO ASP VAL SEQRES 6 A 152 GLU ARG CYS LEU ARG ALA HIS ARG ASN ASP MET GLU THR SEQRES 7 A 152 ILE TYR PRO PHE LEU PHE LEU GLY PHE VAL TYR SER PHE SEQRES 8 A 152 LEU GLY PRO ASN PRO PHE VAL ALA TRP MET HIS PHE LEU SEQRES 9 A 152 VAL PHE LEU VAL GLY ARG VAL ALA HIS THR VAL ALA TYR SEQRES 10 A 152 LEU GLY LYS LEU ARG ALA PRO ILE ARG SER VAL THR TYR SEQRES 11 A 152 THR LEU ALA GLN LEU PRO CYS ALA SER MET ALA LEU GLN SEQRES 12 A 152 ILE LEU TRP GLU ALA ALA ARG HIS LEU HET PLM A 201 14 HET PLM A 202 8 HET 48T A 203 21 HETNAM PLM PALMITIC ACID HETNAM 48T L-GAMMA-GLUTAMYL-S-(2-BIPHENYL-4-YL-2-OXOETHYL)-L- HETNAM 2 48T CYSTEINYLGLYCINE FORMUL 2 PLM 2(C16 H32 O2) FORMUL 4 48T C24 H27 N3 O7 S FORMUL 5 HOH *33(H2 O) HELIX 1 AA1 ALA A 12 LYS A 42 1 31 HELIX 2 AA2 ASN A 46 LEU A 51 1 6 HELIX 3 AA3 ARG A 52 GLY A 54 5 3 HELIX 4 AA4 GLY A 55 CYS A 59 5 5 HELIX 5 AA5 ASP A 62 LEU A 92 1 31 HELIX 6 AA6 ASN A 95 GLY A 119 1 25 HELIX 7 AA7 PRO A 124 ARG A 150 1 27 CISPEP 1 ALA A 123 PRO A 124 0 1.43 CRYST1 77.200 77.200 122.060 90.00 90.00 120.00 H 3 9 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 0.012953 0.007479 0.000000 0.00000 SCALE2 0.000000 0.014957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008193 0.00000