HEADER ISOMERASE 01-MAY-26 26JH TITLE CRYSTAL STRUCTURE OF THE C65A/M94W/M145W/C167A MUTANT OF HUMAN TITLE 2 LIPOCALIN-TYPE 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-2 KEYWDS LIPOCALIN FAMILY, BETA BARREL STRUCTURE, HYDROPHOBIC DRUG, DRUG KEYWDS 2 DELIVERY SYSTEM, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.MUROYA,S.NISHIMURA,T.INUI REVDAT 1 16-SEP-26 26JH 0 JRNL AUTH M.NAKATSUJI,H.MUROYA,R.OKUBO,Y.TERAOKA,M.YAMADA,K.NISHIDE, JRNL AUTH 2 H.YOSHIDA,K.FURUTA,R.KOYAMA,T.KIDA,H.DOI,S.NISHIMURA,T.INUI JRNL TITL DEVELOPMENT OF A DRUG DELIVERY VEHICLE PROTEIN EXHIBITING JRNL TITL 2 HIGH BINDING AFFINITY AND LOW LEAKAGE OF THE ANTI-CANCER JRNL TITL 3 DRUG SN-38. JRNL REF INT.J.BIOL.MACROMOL. V. 381 54313 2026 JRNL REFN ISSN 0141-8130 JRNL PMID 42680028 JRNL DOI 10.1016/J.IJBIOMAC.2026.154313 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 25075 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) : 0.211 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1254 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 32.5400 - 3.1000 1.00 2816 149 0.1991 0.2426 REMARK 3 2 3.1000 - 2.4600 1.00 2688 141 0.2238 0.2563 REMARK 3 3 2.4600 - 2.1500 1.00 2650 140 0.2155 0.2611 REMARK 3 4 2.1500 - 1.9500 1.00 2645 139 0.2125 0.2395 REMARK 3 5 1.9500 - 1.8100 1.00 2624 138 0.2136 0.2550 REMARK 3 6 1.8100 - 1.7000 1.00 2632 139 0.2095 0.2393 REMARK 3 7 1.7000 - 1.6200 1.00 2605 137 0.2134 0.2387 REMARK 3 8 1.6200 - 1.5500 1.00 2600 137 0.2334 0.2543 REMARK 3 9 1.5500 - 1.4900 0.99 2561 134 0.2749 0.3162 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) : 0.198 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.524 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.84 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 : 0.005 1162 REMARK 3 ANGLE : 0.758 1585 REMARK 3 CHIRALITY : 0.071 177 REMARK 3 PLANARITY : 0.004 201 REMARK 3 DIHEDRAL : 25.000 162 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 26JH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAY-26. REMARK 100 THE DEPOSITION ID IS D_1300073753. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS MAR 15, 2019 REMARK 200 DATA SCALING SOFTWARE : XDS MAR 15, 2019 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25079 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : 0.72000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 7.0.078 REMARK 200 STARTING MODEL: 4ORR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NASCN, 30% PEG3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 18.23700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.01450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.33600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.01450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.23700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.33600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 GLY A 21 REMARK 465 SER A 22 REMARK 465 ALA A 23 REMARK 465 PRO A 24 REMARK 465 GLU A 25 REMARK 465 ALA A 26 REMARK 465 GLN A 27 REMARK 465 LEU A 55 REMARK 465 ARG A 56 REMARK 465 GLU A 57 REMARK 465 LYS A 58 REMARK 465 LYS A 59 REMARK 465 ALA A 60 REMARK 465 ALA A 61 REMARK 465 LYS A 137 REMARK 465 GLY A 138 REMARK 465 PRO A 139 REMARK 465 GLY A 140 REMARK 465 GLU A 141 REMARK 465 MET A 187 REMARK 465 THR A 188 REMARK 465 GLU A 189 REMARK 465 GLN A 190 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 52 OG REMARK 470 TRP A 54 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 54 CZ3 CH2 REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 ARG A 108 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 134 CG CD OE1 NE2 REMARK 470 ASP A 142 CG OD1 OD2 REMARK 470 GLU A 174 CG CD OE1 OE2 REMARK 470 ASP A 175 CG OD1 OD2 REMARK 470 GLN A 182 CG CD OE1 NE2 REMARK 470 THR A 183 OG1 CG2 REMARK 470 ASP A 184 CG OD1 OD2 REMARK 470 LYS A 185 CG CD CE NZ 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 LYS A 86 -110.78 54.10 REMARK 500 ALA A 99 -151.85 -97.92 REMARK 500 TYR A 125 -40.58 68.96 REMARK 500 GLN A 127 -46.04 -132.22 REMARK 500 ASP A 184 -68.48 -104.74 REMARK 500 REMARK 500 REMARK: NULL DBREF 26JH A 21 190 UNP P41222 PTGDS_HUMAN 21 190 SEQADV 26JH GLY A 21 UNP P41222 GLN 21 ENGINEERED MUTATION SEQADV 26JH SER A 22 UNP P41222 ALA 22 ENGINEERED MUTATION SEQADV 26JH ALA A 65 UNP P41222 CYS 65 ENGINEERED MUTATION SEQADV 26JH TRP A 94 UNP P41222 MET 94 ENGINEERED MUTATION SEQADV 26JH TRP A 145 UNP P41222 MET 145 ENGINEERED MUTATION SEQADV 26JH 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 TRP 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 TRP 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 FORMUL 2 HOH *91(H2 O) HELIX 1 AA1 GLN A 35 LEU A 40 1 6 HELIX 2 AA2 PRO A 110 GLY A 113 5 4 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 ARG A 144 SER A 150 -1 O ALA A 146 N ALA A 49 SHEET 4 AA110 TYR A 128 GLY A 135 -1 N SER A 133 O TRP A 145 SHEET 5 AA110 SER A 114 THR A 123 -1 N GLU A 122 O LEU A 130 SHEET 6 AA110 SER A 104 SER A 109 -1 N SER A 109 O SER A 114 SHEET 7 AA110 GLN A 88 PRO A 98 -1 N GLN A 97 O SER A 106 SHEET 8 AA110 LEU A 77 ARG A 85 -1 N LEU A 77 O LEU A 96 SHEET 9 AA110 ALA A 65 PRO A 71 -1 N ALA A 70 O ASN A 78 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 2.01 CRYST1 36.474 56.672 72.029 90.00 90.00 90.00 P 21 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 0.027417 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017645 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013883 0.00000 CONECT 405 1132 CONECT 1132 405 MASTER 271 0 0 4 10 0 0 6 1210 1 2 14 END