HEADER ISOMERASE 27-JAN-10 2KTD TITLE SOLUTION STRUCTURE OF MOUSE LIPOCALIN-TYPE PROSTAGLANDIN D SYNTHASE / TITLE 2 SUBSTRATE ANALOG (U-46619) COMPLEX 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-TYPE PROSTAGLANDIN D SYNTHASE, L-PGDS, PROSTAGLANDIN H2, KEYWDS 2 PROSTAGLANDIN D2, U-46619, LIPOCALIN, DISULFIDE BOND, ENDOPLASMIC KEYWDS 3 RETICULUM, FATTY ACID BIOSYNTHESIS, GLYCOPROTEIN, GOLGI APPARATUS, KEYWDS 4 ISOMERASE, LIPID SYNTHESIS, NUCLEUS, PROSTAGLANDIN BIOSYNTHESIS, KEYWDS 5 PYRROLIDONE CARBOXYLIC ACID, SECRETED, TRANSPORT EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR S.SHIMAMOTO,H.MARUO,T.YOSHIDA,N.KATO,T.OHKUBO REVDAT 2 01-MAY-24 2KTD 1 REMARK SEQADV REVDAT 1 02-FEB-11 2KTD 0 JRNL AUTH S.SHIMAMOTO,H.MARUO,T.YOSHIDA,T.INUI,Y.MIYAMOTO,Y.KOBAYASHI, JRNL AUTH 2 T.TSURUMURA,K.ARITAKE,Y.URADE,T.OHKUBO JRNL TITL SOLUTION STRUCTURE OF LIPOCALIN-TYPE PROSTAGLANDIN D JRNL TITL 2 SYNTHASE / SUBSTRATE ANALOG COMPLEX REVEALS OPEN-CLOSED JRNL TITL 3 CONFORMATIONAL CHANGE REQUIRED FOR SUBSTRATE RECOGNITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRVIEW, CNS REMARK 3 AUTHORS : JOHNSON, ONE MOON SCIENTIFIC (NMRVIEW), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KTD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000101549. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300.5 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0MM [U-15N] PROTEIN; 1.5MM 15 REMARK 210 -HYDROXY-11ALPHA,9ALPHA-(EPOXYMETHANO)PROSTA-5,13-DIENOIC ACID; REMARK 210 90% H2O/10% D2O; 1.0MM [U-13C; U-15N] PROTEIN; 1.5MM 15-HYDROXY- REMARK 210 11ALPHA,9ALPHA-(EPOXYMETHANO)PROSTA-5,13-DIENOIC ACID; 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D REMARK 210 HBHA(CO)NH 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 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 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 ASP A 28 160.62 172.09 REMARK 500 1 ASN A 33 46.14 95.96 REMARK 500 1 ALA A 46 -45.57 -138.75 REMARK 500 1 CYS A 65 -160.71 -174.12 REMARK 500 1 ARG A 85 167.78 56.64 REMARK 500 1 LYS A 86 92.54 82.16 REMARK 500 1 ASN A 87 -62.01 68.45 REMARK 500 1 THR A 91 87.97 -166.86 REMARK 500 1 SER A 108 108.62 -52.29 REMARK 500 1 HIS A 111 35.71 159.15 REMARK 500 1 SER A 112 -71.21 74.78 REMARK 500 1 SER A 114 89.79 38.40 REMARK 500 1 GLU A 122 -86.48 -170.88 REMARK 500 1 ALA A 123 130.43 63.92 REMARK 500 1 ASP A 126 7.66 54.54 REMARK 500 1 PRO A 139 -32.34 -38.65 REMARK 500 1 THR A 152 -29.19 -144.76 REMARK 500 1 GLN A 153 42.48 81.65 REMARK 500 1 LEU A 172 -179.64 -52.27 REMARK 500 1 LEU A 180 59.28 30.97 REMARK 500 1 PRO A 181 156.95 -49.99 REMARK 500 1 GLN A 188 48.22 -104.56 REMARK 500 2 ASP A 28 147.55 -176.96 REMARK 500 2 THR A 29 -79.78 -148.13 REMARK 500 2 ASN A 33 59.51 85.18 REMARK 500 2 ALA A 46 -43.19 -158.84 REMARK 500 2 TYR A 63 -159.50 -98.46 REMARK 500 2 CYS A 65 -163.19 -171.59 REMARK 500 2 LEU A 84 104.58 -170.21 REMARK 500 2 ARG A 85 -37.51 179.88 REMARK 500 2 LYS A 86 -66.02 -90.05 REMARK 500 2 ASN A 87 -35.83 -174.16 REMARK 500 2 THR A 91 114.81 -171.69 REMARK 500 2 ILE A 93 113.84 -167.42 REMARK 500 2 SER A 108 102.32 -59.24 REMARK 500 2 HIS A 111 14.98 104.27 REMARK 500 2 SER A 112 -52.13 78.34 REMARK 500 2 SER A 114 78.14 37.31 REMARK 500 2 GLU A 122 -96.03 -171.63 REMARK 500 2 ALA A 123 136.19 66.74 REMARK 500 2 ASP A 126 7.01 59.97 REMARK 500 2 PRO A 139 -33.64 -36.94 REMARK 500 2 THR A 152 -33.33 -161.45 REMARK 500 2 GLN A 153 46.95 81.94 REMARK 500 2 LEU A 172 178.89 -49.51 REMARK 500 2 LEU A 180 94.12 -35.47 REMARK 500 2 PRO A 183 62.14 -67.24 REMARK 500 2 LYS A 185 -80.64 -43.68 REMARK 500 2 ALA A 186 139.24 62.01 REMARK 500 2 GLN A 188 47.48 -96.33 REMARK 500 REMARK 500 THIS ENTRY HAS 371 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PUC A 200 DBREF 2KTD A 25 189 UNP O09114 PTGDS_MOUSE 25 189 SEQADV 2KTD GLY A 23 UNP O09114 EXPRESSION TAG SEQADV 2KTD SER A 24 UNP O09114 EXPRESSION TAG SEQADV 2KTD ALA A 89 UNP O09114 CYS 89 ENGINEERED MUTATION SEQADV 2KTD ALA A 186 UNP O09114 CYS 186 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 CYS 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 ALA 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 ALA ILE GLN GLU HET PUC A 200 59 HETNAM PUC (5Z)-7-{(1R,4S,5S,6R)-6-[(1E,3S)-3-HYDROXYOCT-1-EN-1- HETNAM 2 PUC YL]-2-OXABICYCLO[2.2.1]HEPT-5-YL}HEPT-5-ENOIC ACID HETSYN PUC 15-HYDROXY-11 ALPHA,9 ALPHA-(EPOXYMETHANO)PROSTA-5,13- HETSYN 2 PUC DIENOIC ACID FORMUL 2 PUC C21 H34 O4 HELIX 1 1 GLN A 35 PHE A 39 5 5 HELIX 2 2 PHE A 55 ALA A 60 1 6 HELIX 3 3 LYS A 156 GLY A 171 1 16 SHEET 1 A 9 GLY A 41 SER A 50 0 SHEET 2 A 9 LYS A 66 ALA A 70 -1 O VAL A 69 N GLY A 41 SHEET 3 A 9 LEU A 77 PHE A 83 -1 O THR A 80 N VAL A 68 SHEET 4 A 9 GLU A 90 PRO A 98 -1 O GLU A 90 N PHE A 83 SHEET 5 A 9 TYR A 105 TYR A 107 -1 O THR A 106 N GLN A 97 SHEET 6 A 9 SER A 117 SER A 119 -1 O VAL A 118 N TYR A 105 SHEET 7 A 9 ALA A 129 ARG A 134 -1 O PHE A 132 N SER A 119 SHEET 8 A 9 MET A 145 SER A 150 -1 O THR A 147 N LEU A 131 SHEET 9 A 9 GLY A 41 SER A 50 -1 N GLY A 47 O LEU A 148 SITE 1 AC1 11 SER A 45 LEU A 48 LYS A 58 LEU A 62 SITE 2 AC1 11 TYR A 63 CYS A 65 THR A 67 SER A 81 SITE 3 AC1 11 GLU A 90 TYR A 107 PRO A 110 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