HEADER ISOMERASE 20-DEC-22 8HTA TITLE SOLUTION STRUCTURE OF THE C65A/C167A MUTANT OF HUMAN LIPOCALIN-TYPE TITLE 2 PROSTAGLANDIN D SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROSTAGLANDIN-H2 D-ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-TRACE PROTEIN,CEREBRIN-28,GLUTATHIONE-INDEPENDENT PGD COMPND 5 SYNTHASE,LIPOCALIN-TYPE PROSTAGLANDIN-D SYNTHASE,L-PGDS, COMPND 6 PROSTAGLANDIN-D2 SYNTHASE,PGD2 SYNTHASE,PGDS,PGDS2; COMPND 7 EC: 5.3.99.2; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PTGDS, PDS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS LIPOCALIN, BETA-BARREL, FATTY ACID BIOSYNTHESIS, GLYCOPROTEIN, KEYWDS 2 ISOMERASE, PROSTAGLANDIN BIOSYNTHESIS, SECRETED, TRANSPORT EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.MIYAMOTO,T.INUI REVDAT 3 13-NOV-24 8HTA 1 REMARK REVDAT 2 30-AUG-23 8HTA 1 JRNL REVDAT 1 19-APR-23 8HTA 0 JRNL AUTH Y.MIYAMOTO,M.NAKATSUJI,T.YOSHIDA,T.OHKUBO,T.INUI JRNL TITL STRUCTURAL AND INTERACTION ANALYSIS OF HUMAN LIPOCALIN-TYPE JRNL TITL 2 PROSTAGLANDIN D SYNTHASE WITH THE POORLY WATER-SOLUBLE DRUG JRNL TITL 3 NBQX. JRNL REF FEBS J. V. 290 3983 2023 JRNL REFN ISSN 1742-464X JRNL PMID 37021622 JRNL DOI 10.1111/FEBS.16791 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8HTA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034295. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 308 REMARK 210 PH : 4.0; 4.0 REMARK 210 IONIC STRENGTH : 20; 20 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 20 MM [U-2H] ACETIC ACID, 500 MM REMARK 210 [U-13C; U-15N] PROSTAGLANDIN-H2 REMARK 210 D-ISOMERASE, 10 % [U-99% 2H] D2O, REMARK 210 90% H2O/10% D2O; 20 MM [U-2H] REMARK 210 ACETIC ACID, 500 MM [U-13C; U- REMARK 210 15N] PROSTAGLANDIN-H2 D- REMARK 210 ISOMERASE, 99.95 % [U-100% 2H] REMARK 210 D2O, 99.95% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D 1H-15N NOESY; 3D REMARK 210 1H-15N TOCSY; 2D 13C-1H (HB) REMARK 210 CB(CGCD)HD; 3D HCCH-TOCSY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.115, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 5000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 ASP A 124 H GLN A 127 1.45 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 1 PRO A 24 -161.13 -57.19 REMARK 500 1 GLU A 25 149.22 63.14 REMARK 500 1 ALA A 26 94.05 -176.17 REMARK 500 1 SER A 29 37.67 -175.97 REMARK 500 1 PRO A 32 -149.93 -56.04 REMARK 500 1 ASN A 33 25.88 -74.50 REMARK 500 1 PHE A 34 166.26 -47.64 REMARK 500 1 LEU A 40 -161.75 -71.21 REMARK 500 1 ALA A 46 -69.91 -141.63 REMARK 500 1 SER A 50 -175.99 -174.43 REMARK 500 1 SER A 63 -172.08 -172.73 REMARK 500 1 ARG A 85 130.51 -177.60 REMARK 500 1 ALA A 99 38.08 -93.92 REMARK 500 1 LEU A 102 165.07 -49.91 REMARK 500 1 TYR A 125 -33.31 -36.62 REMARK 500 1 GLN A 127 -55.33 -139.68 REMARK 500 1 PRO A 139 92.00 -51.87 REMARK 500 1 GLU A 141 111.60 60.80 REMARK 500 1 CYS A 186 140.88 -171.52 REMARK 500 2 PRO A 24 -176.40 -52.24 REMARK 500 2 ALA A 26 120.82 -176.32 REMARK 500 2 GLN A 27 39.35 -98.90 REMARK 500 2 SER A 29 37.87 -177.81 REMARK 500 2 PRO A 32 34.42 -84.73 REMARK 500 2 LEU A 40 -163.93 -72.48 REMARK 500 2 ALA A 46 -60.12 -147.06 REMARK 500 2 SER A 52 138.59 -176.57 REMARK 500 2 SER A 63 -172.06 -172.84 REMARK 500 2 ASP A 74 31.53 -99.51 REMARK 500 2 ARG A 85 127.23 -176.76 REMARK 500 2 ALA A 99 39.69 -92.75 REMARK 500 2 LEU A 102 165.20 -49.49 REMARK 500 2 GLU A 122 131.50 -178.75 REMARK 500 2 ASP A 126 -67.25 -106.17 REMARK 500 2 GLN A 127 37.19 176.58 REMARK 500 2 MET A 145 114.26 -164.48 REMARK 500 2 GLU A 189 105.85 61.12 REMARK 500 3 ALA A 23 87.71 -175.01 REMARK 500 3 GLN A 27 43.77 -96.02 REMARK 500 3 VAL A 28 -71.31 -63.69 REMARK 500 3 PRO A 32 -150.25 -56.85 REMARK 500 3 ASN A 33 26.06 -75.28 REMARK 500 3 PHE A 34 166.13 -44.12 REMARK 500 3 LEU A 40 -161.97 -71.20 REMARK 500 3 ALA A 46 -59.85 -137.74 REMARK 500 3 SER A 50 -178.24 -174.85 REMARK 500 3 SER A 63 -172.12 -173.03 REMARK 500 3 ASP A 74 32.11 -99.30 REMARK 500 3 ARG A 85 134.14 -177.45 REMARK 500 3 ALA A 99 39.51 -94.78 REMARK 500 REMARK 500 THIS ENTRY HAS 195 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36532 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE C65A/C167A MUTANT OF HUMAN LIPOCALIN-TYPE REMARK 900 PROSTAGLANDIN D SYNTHASE DBREF 8HTA A 23 190 UNP P41222 PTGDS_HUMAN 23 190 SEQADV 8HTA GLY A 21 UNP P41222 EXPRESSION TAG SEQADV 8HTA SER A 22 UNP P41222 EXPRESSION TAG SEQADV 8HTA ALA A 65 UNP P41222 CYS 65 ENGINEERED MUTATION SEQADV 8HTA ALA A 167 UNP P41222 CYS 167 ENGINEERED MUTATION SEQRES 1 A 170 GLY SER ALA PRO GLU ALA GLN VAL SER VAL GLN PRO ASN SEQRES 2 A 170 PHE GLN GLN ASP LYS PHE LEU GLY ARG TRP PHE SER ALA SEQRES 3 A 170 GLY LEU ALA SER ASN SER SER TRP LEU ARG GLU LYS LYS SEQRES 4 A 170 ALA ALA LEU SER MET ALA LYS SER VAL VAL ALA PRO ALA SEQRES 5 A 170 THR ASP GLY GLY LEU ASN LEU THR SER THR PHE LEU ARG SEQRES 6 A 170 LYS ASN GLN CYS GLU THR ARG THR MET LEU LEU GLN PRO SEQRES 7 A 170 ALA GLY SER LEU GLY SER TYR SER TYR ARG SER PRO HIS SEQRES 8 A 170 TRP GLY SER THR TYR SER VAL SER VAL VAL GLU THR ASP SEQRES 9 A 170 TYR ASP GLN TYR ALA LEU LEU TYR SER GLN GLY SER LYS SEQRES 10 A 170 GLY PRO GLY GLU ASP PHE ARG MET ALA THR LEU TYR SER SEQRES 11 A 170 ARG THR GLN THR PRO ARG ALA GLU LEU LYS GLU LYS PHE SEQRES 12 A 170 THR ALA PHE ALA LYS ALA GLN GLY PHE THR GLU ASP THR SEQRES 13 A 170 ILE VAL PHE LEU PRO GLN THR ASP LYS CYS MET THR GLU SEQRES 14 A 170 GLN HELIX 1 AA1 GLN A 35 PHE A 39 5 5 HELIX 2 AA2 SER A 53 ALA A 60 1 8 HELIX 3 AA3 ARG A 156 GLN A 170 1 15 HELIX 4 AA4 THR A 173 ASP A 175 5 3 SHEET 1 AA110 ILE A 177 PHE A 179 0 SHEET 2 AA110 GLY A 41 ALA A 49 -1 N LEU A 48 O VAL A 178 SHEET 3 AA110 PHE A 143 SER A 150 -1 O SER A 150 N PHE A 44 SHEET 4 AA110 TYR A 128 SER A 136 -1 N SER A 133 O MET A 145 SHEET 5 AA110 SER A 114 ASP A 124 -1 N SER A 119 O TYR A 132 SHEET 6 AA110 SER A 104 SER A 109 -1 N TYR A 105 O VAL A 118 SHEET 7 AA110 CYS A 89 PRO A 98 -1 N GLN A 97 O SER A 106 SHEET 8 AA110 LEU A 77 LEU A 84 -1 N LEU A 77 O LEU A 96 SHEET 9 AA110 ALA A 65 VAL A 69 -1 N VAL A 68 O THR A 80 SHEET 10 AA110 GLY A 41 ALA A 49 -1 N TRP A 43 O SER A 67 SSBOND 1 CYS A 89 CYS A 186 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1