HEADER ISOMERASE 24-DEC-08 2RQ0 TITLE SOLUTION STRUCTURE OF MOUSE LIPOCALIN-TYPE PROSTAGLANDIN D SYNTHASE TITLE 2 POSSESSING THE INTRINSIC DISULFIDE BOND COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROSTAGLANDIN-H2 D-ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LIPOCALIN-TYPE PROSTAGLANDIN-D SYNTHASE, GLUTATHIONE- COMPND 5 INDEPENDENT PGD SYNTHETASE, PROSTAGLANDIN-D2 SYNTHASE, PGD2 SYNTHASE, COMPND 6 PGDS2, PGDS; COMPND 7 EC: 5.3.99.2; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PTGDS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-2T KEYWDS LIPOCALIN, BETA-BARREL, CYTOPLASM, ENDOPLASMIC RETICULUM, FATTY ACID KEYWDS 2 BIOSYNTHESIS, GLYCOPROTEIN, GOLGI APPARATUS, ISOMERASE, LIPID KEYWDS 3 SYNTHESIS, MEMBRANE, NUCLEUS, PROSTAGLANDIN BIOSYNTHESIS, KEYWDS 4 PYRROLIDONE CARBOXYLIC ACID, SECRETED, TRANSPORT EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.MIYAMOTO,S.NISHIMURA,T.INUI REVDAT 5 30-OCT-24 2RQ0 1 REMARK REVDAT 4 14-JUN-23 2RQ0 1 REMARK REVDAT 3 10-NOV-21 2RQ0 1 SEQADV REVDAT 2 26-FEB-20 2RQ0 1 REMARK SEQADV REVDAT 1 15-DEC-09 2RQ0 0 JRNL AUTH Y.MIYAMOTO,S.NISHIMURA,K.INOUE,S.SHIMAMOTO,T.YOSHIDA, JRNL AUTH 2 A.FUKUHARA,M.YAMADA,Y.URADE,N.YAGI,T.OHKUBO,T.INUI JRNL TITL STRUCTURAL ANALYSIS OF LIPOCALIN-TYPE PROSTAGLANDIN D JRNL TITL 2 SYNTHASE COMPLEXED WITH BILIVERDIN BY SMALL-ANGLE X-RAY JRNL TITL 3 SCATTERING AND MULTI-DIMENSIONAL NMR. JRNL REF J.STRUCT.BIOL. 2009 JRNL REFN ESSN 1095-8657 JRNL PMID 19833210 JRNL DOI 10.1016/J.JSB.2009.10.005 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RQ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000150146. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4 REMARK 210 IONIC STRENGTH : 0.02 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-13C; U-15N] REMARK 210 PROSTAGLANDIN-H2 D-ISOMERASE-1, REMARK 210 20 MM [U-2H] ACETIC ACID-2, 90% REMARK 210 H2O/10% D2O; 0.5 MM [U-13C; U- REMARK 210 15N] PROSTAGLANDIN-H2 D- REMARK 210 ISOMERASE-3, 20 MM [U-2H] ACETIC REMARK 210 ACID-4, 99.9% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-15N TOCSY; 3D REMARK 210 1H-13C NOESY 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 : CNS 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 3000 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 LYS A 156 H LYS A 160 1.51 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 GLN A 25 162.69 59.72 REMARK 500 1 HIS A 27 79.09 -167.98 REMARK 500 1 ASP A 28 37.17 -163.63 REMARK 500 1 ASN A 33 95.49 -177.11 REMARK 500 1 LEU A 40 130.74 -171.36 REMARK 500 1 SER A 45 73.88 -66.21 REMARK 500 1 LEU A 62 96.13 61.74 REMARK 500 1 ALA A 99 41.64 -108.37 REMARK 500 1 HIS A 111 -167.43 -178.97 REMARK 500 1 ASP A 126 -69.82 -104.34 REMARK 500 1 GLU A 127 32.22 -174.40 REMARK 500 1 LYS A 137 80.72 58.27 REMARK 500 1 PRO A 139 48.08 -78.39 REMARK 500 1 ASP A 142 86.97 49.80 REMARK 500 1 ASP A 184 -58.35 -165.96 REMARK 500 1 LYS A 185 108.53 61.53 REMARK 500 2 SER A 24 38.31 -97.33 REMARK 500 2 ASP A 28 119.93 -177.31 REMARK 500 2 ASN A 33 77.24 -176.17 REMARK 500 2 SER A 45 94.45 -53.96 REMARK 500 2 LEU A 62 107.04 56.93 REMARK 500 2 LYS A 86 73.92 39.34 REMARK 500 2 ALA A 99 43.46 -95.41 REMARK 500 2 HIS A 111 -71.07 -132.15 REMARK 500 2 ASN A 124 74.79 -64.58 REMARK 500 2 GLU A 127 -84.26 -153.72 REMARK 500 2 PRO A 139 46.93 -75.55 REMARK 500 2 ASP A 142 79.83 43.63 REMARK 500 2 THR A 154 -161.77 -119.81 REMARK 500 2 PRO A 181 -164.74 -71.20 REMARK 500 2 CYS A 186 -156.94 -101.87 REMARK 500 3 SER A 24 100.24 60.20 REMARK 500 3 GLN A 25 93.83 60.38 REMARK 500 3 HIS A 27 -45.33 -148.46 REMARK 500 3 PRO A 32 -173.27 -58.80 REMARK 500 3 LEU A 40 94.37 -67.14 REMARK 500 3 SER A 45 92.74 -56.73 REMARK 500 3 SER A 53 24.16 -141.45 REMARK 500 3 LEU A 62 126.88 71.07 REMARK 500 3 LYS A 86 71.36 45.62 REMARK 500 3 ALA A 99 40.15 -102.37 REMARK 500 3 HIS A 111 -80.19 -93.82 REMARK 500 3 ASN A 124 78.24 -63.88 REMARK 500 3 ASP A 126 30.65 72.67 REMARK 500 3 GLU A 127 -77.82 -157.11 REMARK 500 3 LYS A 137 98.69 41.11 REMARK 500 3 ASP A 142 83.37 46.20 REMARK 500 3 THR A 154 -162.19 -116.22 REMARK 500 3 PRO A 181 -159.25 -63.90 REMARK 500 3 ASP A 184 65.88 -179.97 REMARK 500 REMARK 500 THIS ENTRY HAS 167 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11062 RELATED DB: BMRB DBREF 2RQ0 A 25 189 UNP O09114 PTGDS_MOUSE 25 189 SEQADV 2RQ0 GLY A 23 UNP O09114 EXPRESSION TAG SEQADV 2RQ0 SER A 24 UNP O09114 EXPRESSION TAG SEQADV 2RQ0 ALA A 65 UNP O09114 CYS 65 ENGINEERED MUTATION SEQRES 1 A 167 GLY SER GLN GLY HIS ASP THR VAL GLN PRO ASN PHE GLN SEQRES 2 A 167 GLN ASP LYS PHE LEU GLY ARG TRP TYR SER ALA GLY LEU SEQRES 3 A 167 ALA SER ASN SER SER TRP PHE ARG GLU LYS LYS ALA VAL SEQRES 4 A 167 LEU TYR MET ALA LYS THR VAL VAL ALA PRO SER THR GLU SEQRES 5 A 167 GLY GLY LEU ASN LEU THR SER THR PHE LEU ARG LYS ASN SEQRES 6 A 167 GLN CYS GLU THR LYS ILE MET VAL LEU GLN PRO ALA GLY SEQRES 7 A 167 ALA PRO GLY HIS TYR THR TYR SER SER PRO HIS SER GLY SEQRES 8 A 167 SER ILE HIS SER VAL SER VAL VAL GLU ALA ASN TYR ASP SEQRES 9 A 167 GLU TYR ALA LEU LEU PHE SER ARG GLY THR LYS GLY PRO SEQRES 10 A 167 GLY GLN ASP PHE ARG MET ALA THR LEU TYR SER ARG THR SEQRES 11 A 167 GLN THR LEU LYS ASP GLU LEU LYS GLU LYS PHE THR THR SEQRES 12 A 167 PHE SER LYS ALA GLN GLY LEU THR GLU GLU ASP ILE VAL SEQRES 13 A 167 PHE LEU PRO GLN PRO ASP LYS CYS ILE GLN GLU HELIX 1 1 GLN A 35 LEU A 40 1 6 HELIX 2 2 SER A 53 ALA A 60 1 8 HELIX 3 3 LYS A 156 GLY A 171 1 16 SHEET 1 A10 GLY A 41 ALA A 49 0 SHEET 2 A10 MET A 64 PRO A 71 -1 O THR A 67 N TRP A 43 SHEET 3 A10 LEU A 77 LEU A 84 -1 O THR A 82 N LYS A 66 SHEET 4 A10 CYS A 89 PRO A 98 -1 O GLU A 90 N PHE A 83 SHEET 5 A10 HIS A 104 SER A 109 -1 O THR A 106 N GLN A 97 SHEET 6 A10 SER A 114 ALA A 123 -1 O VAL A 118 N TYR A 105 SHEET 7 A10 TYR A 128 GLY A 135 -1 O LEU A 130 N GLU A 122 SHEET 8 A10 PHE A 143 SER A 150 -1 O THR A 147 N LEU A 131 SHEET 9 A10 LEU A 48 SER A 50 -1 N ALA A 49 O ALA A 146 SHEET 10 A10 ILE A 177 VAL A 178 -1 O VAL A 178 N LEU A 48 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