HEADER TRANSFERASE 29-AUG-17 5Y9Z TITLE CRYSTAL STRUCTURE OF RAT HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: H-PGDS,GST CLASS-SIGMA,GLUTATHIONE S-TRANSFERASE, COMPND 5 GLUTATHIONE-DEPENDENT PGD SYNTHASE,GLUTATHIONE-REQUIRING COMPND 6 PROSTAGLANDIN D SYNTHASE,PROSTAGLANDIN-H2 D-ISOMERASE; COMPND 7 EC: 5.3.99.2,2.5.1.18; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: HPGDS, GSTS, PGDS, PTGDS2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROSTAGLANDIN D SYNTHASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KAMO,N.FURUBAYASHI,K.INAKA,H.TANAKA,K.ARITAKE,Y.URADE REVDAT 2 22-NOV-23 5Y9Z 1 REMARK LINK REVDAT 1 19-SEP-18 5Y9Z 0 JRNL AUTH M.KAMO,N.FURUBAYASHI,K.INAKA,H.TANAKA,K.ARITAKE,Y.URADE JRNL TITL CRYSTAL STRUCTURE OF RAT HEMATOPOIETIC PROSTAGLANDIN D JRNL TITL 2 SYNTHASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 166098 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 8782 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 12137 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 636 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3280 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 523 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.52000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : -0.44000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.030 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.030 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.022 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.065 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3463 ; 0.008 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3290 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4681 ; 1.416 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7630 ; 0.937 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 394 ; 5.305 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;34.880 ;24.051 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 590 ;11.254 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;12.846 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 517 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3686 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 706 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6745 ; 1.937 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 332 ;21.730 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6861 ; 6.965 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5Y9Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1300004911. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 175007 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.090 REMARK 200 RESOLUTION RANGE LOW (A) : 48.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.52900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1PD2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS-HCL, PH 8.5, 35% PEG6000, 5 REMARK 280 MM DTT, 5MM GSH, 2 MM DIOXANE, 2 MM MGCL2, LIQUID DIFFUSION, REMARK 280 TEMPERATURE 293K 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 27.27000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.92000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.27000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.92000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 MET B 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 551 O HOH B 370 1455 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 14 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 14 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 33 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 33 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES 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 GLN A 63 108.63 76.55 REMARK 500 LYS A 164 88.37 -151.02 REMARK 500 GLN B 63 108.56 77.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 574 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A 575 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A 576 DISTANCE = 8.59 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 321 O REMARK 620 2 HOH A 341 O 95.7 REMARK 620 3 HOH A 353 O 93.6 89.1 REMARK 620 4 HOH B 341 O 84.2 93.5 176.7 REMARK 620 5 HOH B 343 O 89.8 172.4 85.3 92.3 REMARK 620 6 HOH B 349 O 175.2 85.3 91.2 91.1 89.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 381 O REMARK 620 2 HOH A 386 O 86.2 REMARK 620 3 HOH A 390 O 89.5 88.0 REMARK 620 4 HOH A 513 O 91.7 176.6 89.3 REMARK 620 5 HOH A 532 O 178.4 93.0 89.1 89.0 REMARK 620 6 HOH A 563 O 91.6 96.2 175.7 86.5 89.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GSH A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DIO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DIO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GSH B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DIO B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DIO B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 206 DBREF 5Y9Z A 1 199 UNP O35543 HPGDS_RAT 1 199 DBREF 5Y9Z B 1 199 UNP O35543 HPGDS_RAT 1 199 SEQRES 1 A 199 MET PRO ASN TYR LYS LEU LEU TYR PHE ASN MET ARG GLY SEQRES 2 A 199 ARG ALA GLU ILE ILE ARG TYR ILE PHE ALA TYR LEU ASP SEQRES 3 A 199 ILE LYS TYR GLU ASP HIS ARG ILE GLU GLN ALA ASP TRP SEQRES 4 A 199 PRO LYS ILE LYS PRO THR LEU PRO PHE GLY LYS ILE PRO SEQRES 5 A 199 VAL LEU GLU VAL GLU GLY LEU THR LEU HIS GLN SER LEU SEQRES 6 A 199 ALA ILE ALA ARG TYR LEU THR LYS ASN THR ASP LEU ALA SEQRES 7 A 199 GLY LYS THR GLU LEU GLU GLN CYS GLN VAL ASP ALA VAL SEQRES 8 A 199 VAL ASP THR LEU ASP ASP PHE MET SER LEU PHE PRO TRP SEQRES 9 A 199 ALA GLU GLU ASN GLN ASP LEU LYS GLU ARG THR PHE ASN SEQRES 10 A 199 ASP LEU LEU THR ARG GLN ALA PRO HIS LEU LEU LYS ASP SEQRES 11 A 199 LEU ASP THR TYR LEU GLY ASP LYS GLU TRP PHE ILE GLY SEQRES 12 A 199 ASN TYR VAL THR TRP ALA ASP PHE TYR TRP ASP ILE CYS SEQRES 13 A 199 SER THR THR LEU LEU VAL LEU LYS PRO ASP LEU LEU GLY SEQRES 14 A 199 ILE TYR PRO ARG LEU VAL SER LEU ARG ASN LYS VAL GLN SEQRES 15 A 199 ALA ILE PRO ALA ILE SER ALA TRP ILE LEU LYS ARG PRO SEQRES 16 A 199 GLN THR LYS LEU SEQRES 1 B 199 MET PRO ASN TYR LYS LEU LEU TYR PHE ASN MET ARG GLY SEQRES 2 B 199 ARG ALA GLU ILE ILE ARG TYR ILE PHE ALA TYR LEU ASP SEQRES 3 B 199 ILE LYS TYR GLU ASP HIS ARG ILE GLU GLN ALA ASP TRP SEQRES 4 B 199 PRO LYS ILE LYS PRO THR LEU PRO PHE GLY LYS ILE PRO SEQRES 5 B 199 VAL LEU GLU VAL GLU GLY LEU THR LEU HIS GLN SER LEU SEQRES 6 B 199 ALA ILE ALA ARG TYR LEU THR LYS ASN THR ASP LEU ALA SEQRES 7 B 199 GLY LYS THR GLU LEU GLU GLN CYS GLN VAL ASP ALA VAL SEQRES 8 B 199 VAL ASP THR LEU ASP ASP PHE MET SER LEU PHE PRO TRP SEQRES 9 B 199 ALA GLU GLU ASN GLN ASP LEU LYS GLU ARG THR PHE ASN SEQRES 10 B 199 ASP LEU LEU THR ARG GLN ALA PRO HIS LEU LEU LYS ASP SEQRES 11 B 199 LEU ASP THR TYR LEU GLY ASP LYS GLU TRP PHE ILE GLY SEQRES 12 B 199 ASN TYR VAL THR TRP ALA ASP PHE TYR TRP ASP ILE CYS SEQRES 13 B 199 SER THR THR LEU LEU VAL LEU LYS PRO ASP LEU LEU GLY SEQRES 14 B 199 ILE TYR PRO ARG LEU VAL SER LEU ARG ASN LYS VAL GLN SEQRES 15 B 199 ALA ILE PRO ALA ILE SER ALA TRP ILE LEU LYS ARG PRO SEQRES 16 B 199 GLN THR LYS LEU HET GSH A 201 20 HET MG A 202 1 HET MG A 203 1 HET DIO A 204 6 HET DIO A 205 6 HET EDO A 206 4 HET EDO A 207 4 HET EDO A 208 4 HET GOL A 209 6 HET GSH B 201 20 HET DIO B 202 6 HET DIO B 203 6 HET PGE B 204 10 HET PGE B 205 10 HET EDO B 206 4 HETNAM GSH GLUTATHIONE HETNAM MG MAGNESIUM ION HETNAM DIO 1,4-DIETHYLENE DIOXIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM PGE TRIETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GSH 2(C10 H17 N3 O6 S) FORMUL 4 MG 2(MG 2+) FORMUL 6 DIO 4(C4 H8 O2) FORMUL 8 EDO 4(C2 H6 O2) FORMUL 11 GOL C3 H8 O3 FORMUL 15 PGE 2(C6 H14 O4) FORMUL 18 HOH *523(H2 O) HELIX 1 AA1 ARG A 12 ARG A 14 5 3 HELIX 2 AA2 ALA A 15 ASP A 26 1 12 HELIX 3 AA3 GLU A 35 ALA A 37 5 3 HELIX 4 AA4 ASP A 38 LYS A 43 1 6 HELIX 5 AA5 PRO A 44 LEU A 46 5 3 HELIX 6 AA6 GLN A 63 LYS A 73 1 11 HELIX 7 AA7 THR A 75 GLY A 79 5 5 HELIX 8 AA8 THR A 81 SER A 100 1 20 HELIX 9 AA9 ASN A 108 ARG A 122 1 15 HELIX 10 AB1 GLN A 123 GLY A 136 1 14 HELIX 11 AB2 THR A 147 LYS A 164 1 18 HELIX 12 AB3 TYR A 171 ALA A 183 1 13 HELIX 13 AB4 ILE A 184 ARG A 194 1 11 HELIX 14 AB5 ARG B 12 ARG B 14 5 3 HELIX 15 AB6 ALA B 15 ASP B 26 1 12 HELIX 16 AB7 GLU B 35 ALA B 37 5 3 HELIX 17 AB8 ASP B 38 LYS B 43 1 6 HELIX 18 AB9 PRO B 44 LEU B 46 5 3 HELIX 19 AC1 GLN B 63 LYS B 73 1 11 HELIX 20 AC2 THR B 75 GLY B 79 5 5 HELIX 21 AC3 THR B 81 SER B 100 1 20 HELIX 22 AC4 ASN B 108 ARG B 122 1 15 HELIX 23 AC5 GLN B 123 GLY B 136 1 14 HELIX 24 AC6 THR B 147 LYS B 164 1 18 HELIX 25 AC7 TYR B 171 ILE B 184 1 14 HELIX 26 AC8 ILE B 184 ARG B 194 1 11 SHEET 1 AA1 4 GLU A 30 ILE A 34 0 SHEET 2 AA1 4 LYS A 5 PHE A 9 1 N LEU A 6 O GLU A 30 SHEET 3 AA1 4 VAL A 53 VAL A 56 -1 O GLU A 55 N LYS A 5 SHEET 4 AA1 4 LEU A 59 HIS A 62 -1 O LEU A 61 N LEU A 54 SHEET 1 AA2 4 GLU B 30 ILE B 34 0 SHEET 2 AA2 4 TYR B 4 PHE B 9 1 N LEU B 6 O GLU B 30 SHEET 3 AA2 4 VAL B 53 VAL B 56 -1 O GLU B 55 N LYS B 5 SHEET 4 AA2 4 LEU B 59 HIS B 62 -1 O LEU B 61 N LEU B 54 LINK MG MG A 202 O HOH A 321 1555 1555 1.99 LINK MG MG A 202 O HOH A 341 1555 1555 2.08 LINK MG MG A 202 O HOH A 353 1555 1555 2.07 LINK MG MG A 202 O HOH B 341 1555 1555 2.05 LINK MG MG A 202 O HOH B 343 1555 1555 1.97 LINK MG MG A 202 O HOH B 349 1555 1555 2.07 LINK MG MG A 203 O HOH A 381 1555 1555 2.04 LINK MG MG A 203 O HOH A 386 1555 1555 2.04 LINK MG MG A 203 O HOH A 390 1555 1555 2.08 LINK MG MG A 203 O HOH A 513 1555 1555 2.09 LINK MG MG A 203 O HOH A 532 1555 1555 2.08 LINK MG MG A 203 O HOH A 563 1555 1555 2.07 CISPEP 1 ILE A 51 PRO A 52 0 9.70 CISPEP 2 ILE B 51 PRO B 52 0 9.36 SITE 1 AC1 16 TYR A 8 ARG A 14 TRP A 39 LYS A 43 SITE 2 AC1 16 LYS A 50 ILE A 51 GLN A 63 SER A 64 SITE 3 AC1 16 HOH A 335 HOH A 367 HOH A 406 HOH A 415 SITE 4 AC1 16 HOH A 424 HOH A 445 HOH A 475 ASP B 97 SITE 1 AC2 6 HOH A 321 HOH A 341 HOH A 353 HOH B 341 SITE 2 AC2 6 HOH B 343 HOH B 349 SITE 1 AC3 6 HOH A 381 HOH A 386 HOH A 390 HOH A 513 SITE 2 AC3 6 HOH A 532 HOH A 563 SITE 1 AC4 3 GLY A 13 DIO A 205 HOH A 515 SITE 1 AC5 5 MET A 99 TYR A 152 ILE A 155 DIO A 204 SITE 2 AC5 5 HOH A 389 SITE 1 AC6 6 ASN A 144 GOL A 209 LYS B 41 ILE B 42 SITE 2 AC6 6 THR B 45 HOH B 500 SITE 1 AC7 7 ASN A 10 ARG A 33 GLU A 35 HOH A 325 SITE 2 AC7 7 HOH A 355 ASN B 10 GLU B 35 SITE 1 AC8 8 ALA A 183 PRO A 185 HOH A 317 HOH A 332 SITE 2 AC8 8 HOH A 402 HOH A 567 HOH A 570 HOH B 377 SITE 1 AC9 11 GLU A 139 TRP A 140 ASN A 144 TYR A 145 SITE 2 AC9 11 EDO A 206 HOH A 319 HOH A 338 HOH A 443 SITE 3 AC9 11 HOH A 463 HOH A 467 THR B 45 SITE 1 AD1 14 ASP A 97 TYR B 8 ARG B 14 TRP B 39 SITE 2 AD1 14 LYS B 43 LYS B 50 ILE B 51 GLN B 63 SITE 3 AD1 14 SER B 64 HOH B 325 HOH B 373 HOH B 383 SITE 4 AD1 14 HOH B 398 HOH B 408 SITE 1 AD2 5 MET B 99 TYR B 152 ILE B 155 DIO B 203 SITE 2 AD2 5 HOH B 372 SITE 1 AD3 3 GLY B 13 DIO B 202 HOH B 502 SITE 1 AD4 6 LEU A 83 ASN A 179 VAL B 56 GLU B 57 SITE 2 AD4 6 HOH B 323 HOH B 450 SITE 1 AD5 2 TYR B 24 LEU B 25 SITE 1 AD6 8 PRO A 125 ASP A 166 LEU A 167 TYR A 171 SITE 2 AD6 8 HOH A 468 HOH A 478 VAL B 175 ASN B 179 CRYST1 54.540 79.840 96.600 90.00 90.00 90.00 P 21 21 21 8 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 0.018335 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010352 0.00000