HEADER ISOMERASE 24-MAR-14 4PXQ TITLE CRYSTAL STRUCTURE OF D-GLUCURONYL C5-EPIMERASE IN COMPLEX WITH HEPARIN TITLE 2 HEXASACCHARIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-GLUCURONYL C5 EPIMERASE B; COMPND 3 CHAIN: A, B; COMPND 4 EC: 5.1.3.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: GLCE, GLCEB, HSEPI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSUMO KEYWDS EPIMERIZATION ENZYME, MULTIPLE DOMAIN STRUCTURE, HEPARAN SULFATE C5- KEYWDS 2 EPIMERASE, HEPARIN, HEPARAN SULFATE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.KE,Y.QIN,X.GU,J.TAN,J.S.BRUNZELLE,H.E.XU,K.DING REVDAT 5 28-FEB-24 4PXQ 1 HETSYN REVDAT 4 29-JUL-20 4PXQ 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 18-MAR-15 4PXQ 1 JRNL REVDAT 2 25-FEB-15 4PXQ 1 JRNL REVDAT 1 14-JAN-15 4PXQ 0 JRNL AUTH Y.QIN,J.KE,X.GU,J.FANG,W.WANG,Q.CONG,J.LI,J.TAN, JRNL AUTH 2 J.S.BRUNZELLE,C.ZHANG,Y.JIANG,K.MELCHER,J.P.LI,H.E.XU,K.DING JRNL TITL STRUCTURAL AND FUNCTIONAL STUDY OF D-GLUCURONYL JRNL TITL 2 C5-EPIMERASE. JRNL REF J.BIOL.CHEM. V. 290 4620 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 25568314 JRNL DOI 10.1074/JBC.M114.602201 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 70265 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3728 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5089 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE SET COUNT : 278 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8252 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 210 REMARK 3 SOLVENT ATOMS : 813 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : 0.05000 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): 0.230 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.117 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8682 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11813 ; 1.262 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1029 ; 5.781 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 388 ;34.842 ;22.887 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1422 ;14.454 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 64 ;17.510 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1308 ; 0.206 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6482 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 4122 ; 1.441 ; 2.718 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5149 ; 2.457 ; 4.073 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4558 ; 1.973 ; 2.997 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): 38297 ; 6.391 ;25.645 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4PXQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000085350. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74069 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.29200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 1.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% W/V PEG 3,350, 0.1 M SODIUM REMARK 280 CITRATE TRIBASIC DEHYDRATE PH 5.6, AND 2% V/V TACSIMATE PH 5.0., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 76.30300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 100.49100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 76.30300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 100.49100 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: 11960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 ARG A 2 REMARK 465 CYS A 3 REMARK 465 LEU A 4 REMARK 465 ALA A 5 REMARK 465 ALA A 6 REMARK 465 GLY A 7 REMARK 465 VAL A 8 REMARK 465 HIS A 9 REMARK 465 TYR A 10 REMARK 465 LYS A 11 REMARK 465 THR A 12 REMARK 465 LEU A 13 REMARK 465 ILE A 14 REMARK 465 VAL A 15 REMARK 465 ILE A 16 REMARK 465 CYS A 17 REMARK 465 ALA A 18 REMARK 465 LEU A 19 REMARK 465 LEU A 20 REMARK 465 SER A 21 REMARK 465 LEU A 22 REMARK 465 LEU A 23 REMARK 465 THR A 24 REMARK 465 VAL A 25 REMARK 465 LEU A 26 REMARK 465 LEU A 27 REMARK 465 TRP A 28 REMARK 465 ASN A 29 REMARK 465 LYS A 30 REMARK 465 CYS A 31 REMARK 465 THR A 32 REMARK 465 SER A 33 REMARK 465 GLU A 34 REMARK 465 LYS A 35 REMARK 465 ALA A 36 REMARK 465 LEU A 37 REMARK 465 ARG A 38 REMARK 465 PHE A 39 REMARK 465 LEU A 40 REMARK 465 PRO A 41 REMARK 465 GLN A 42 REMARK 465 HIS A 43 REMARK 465 PRO A 44 REMARK 465 GLN A 45 REMARK 465 PRO A 46 REMARK 465 PRO A 47 REMARK 465 PRO A 48 REMARK 465 SER A 49 REMARK 465 PRO A 50 REMARK 465 LYS A 51 REMARK 465 ILE A 52 REMARK 465 ASP A 53 REMARK 465 SER A 54 REMARK 465 HIS A 55 REMARK 465 PRO A 56 REMARK 465 GLN A 57 REMARK 465 GLN A 58 REMARK 465 PRO A 59 REMARK 465 GLN A 60 REMARK 465 PRO A 61 REMARK 465 PRO A 62 REMARK 465 GLU A 63 REMARK 465 PRO A 64 REMARK 465 PRO A 65 REMARK 465 PRO A 66 REMARK 465 VAL A 67 REMARK 465 VAL A 68 REMARK 465 GLY A 69 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 CYS B 3 REMARK 465 LEU B 4 REMARK 465 ALA B 5 REMARK 465 ALA B 6 REMARK 465 GLY B 7 REMARK 465 VAL B 8 REMARK 465 HIS B 9 REMARK 465 TYR B 10 REMARK 465 LYS B 11 REMARK 465 THR B 12 REMARK 465 LEU B 13 REMARK 465 ILE B 14 REMARK 465 VAL B 15 REMARK 465 ILE B 16 REMARK 465 CYS B 17 REMARK 465 ALA B 18 REMARK 465 LEU B 19 REMARK 465 LEU B 20 REMARK 465 SER B 21 REMARK 465 LEU B 22 REMARK 465 LEU B 23 REMARK 465 THR B 24 REMARK 465 VAL B 25 REMARK 465 LEU B 26 REMARK 465 LEU B 27 REMARK 465 TRP B 28 REMARK 465 ASN B 29 REMARK 465 LYS B 30 REMARK 465 CYS B 31 REMARK 465 THR B 32 REMARK 465 SER B 33 REMARK 465 GLU B 34 REMARK 465 LYS B 35 REMARK 465 ALA B 36 REMARK 465 LEU B 37 REMARK 465 ARG B 38 REMARK 465 PHE B 39 REMARK 465 LEU B 40 REMARK 465 PRO B 41 REMARK 465 GLN B 42 REMARK 465 HIS B 43 REMARK 465 PRO B 44 REMARK 465 GLN B 45 REMARK 465 PRO B 46 REMARK 465 PRO B 47 REMARK 465 PRO B 48 REMARK 465 SER B 49 REMARK 465 PRO B 50 REMARK 465 LYS B 51 REMARK 465 ILE B 52 REMARK 465 ASP B 53 REMARK 465 SER B 54 REMARK 465 HIS B 55 REMARK 465 PRO B 56 REMARK 465 GLN B 57 REMARK 465 GLN B 58 REMARK 465 PRO B 59 REMARK 465 GLN B 60 REMARK 465 PRO B 61 REMARK 465 PRO B 62 REMARK 465 GLU B 63 REMARK 465 PRO B 64 REMARK 465 PRO B 65 REMARK 465 PRO B 66 REMARK 465 VAL B 67 REMARK 465 VAL B 68 REMARK 465 GLY B 69 REMARK 465 GLY B 70 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 ASP A 83 -88.37 -115.25 REMARK 500 SER A 128 152.67 86.21 REMARK 500 MET A 144 -124.58 50.53 REMARK 500 ASP A 302 -122.81 52.84 REMARK 500 ASN A 460 17.19 58.49 REMARK 500 LYS A 461 -41.67 -132.29 REMARK 500 SER A 524 3.11 -153.43 REMARK 500 ASP B 83 -87.93 -114.73 REMARK 500 MET B 144 -123.72 53.31 REMARK 500 ASP B 302 -118.14 59.92 REMARK 500 ASN B 460 11.16 59.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PW2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D-GLUCURONYL C5-EPIMERASE DBREF 4PXQ A 1 585 UNP Q6TS32 Q6TS32_DANRE 1 585 DBREF 4PXQ B 1 585 UNP Q6TS32 Q6TS32_DANRE 1 585 SEQRES 1 A 585 MET ARG CYS LEU ALA ALA GLY VAL HIS TYR LYS THR LEU SEQRES 2 A 585 ILE VAL ILE CYS ALA LEU LEU SER LEU LEU THR VAL LEU SEQRES 3 A 585 LEU TRP ASN LYS CYS THR SER GLU LYS ALA LEU ARG PHE SEQRES 4 A 585 LEU PRO GLN HIS PRO GLN PRO PRO PRO SER PRO LYS ILE SEQRES 5 A 585 ASP SER HIS PRO GLN GLN PRO GLN PRO PRO GLU PRO PRO SEQRES 6 A 585 PRO VAL VAL GLY GLY VAL ARG TYR GLU GLU ILE ASP CYS SEQRES 7 A 585 LEU ILE ASN ASP ASP ALA THR ILE LYS GLY ARG ARG GLU SEQRES 8 A 585 GLY SER GLU VAL TYR MET PRO PHE SER TRP MET GLU LYS SEQRES 9 A 585 TYR PHE GLU VAL TYR GLY LYS VAL VAL GLN TYR ASP GLY SEQRES 10 A 585 TYR ASP ARG PHE GLU PHE SER HIS SER TYR SER LYS VAL SEQRES 11 A 585 TYR ALA GLN ARG GLU GLN TYR HIS PRO ASN GLY VAL PHE SEQRES 12 A 585 MET SER PHE GLU GLY TYR ASN VAL GLU VAL ARG ASP ARG SEQRES 13 A 585 VAL LYS CYS ILE SER GLY VAL GLU GLY VAL PRO LEU SER SEQRES 14 A 585 THR GLN TRP GLY PRO GLN GLY TYR PHE TYR ALA ILE GLN SEQRES 15 A 585 ILE ALA GLN TYR GLY LEU SER HIS TYR SER LYS ASN LEU SEQRES 16 A 585 THR GLU ARG PRO PRO HIS VAL GLU VAL TYR ASP THR ALA SEQRES 17 A 585 GLU GLU ARG ASP SER ARG SER SER ALA TRP THR VAL PRO SEQRES 18 A 585 LYS GLY CYS SER LEU THR ARG VAL TYR ASP LYS THR ARG SEQRES 19 A 585 ALA THR SER VAL ARG GLU PHE SER ALA PRO GLU ASN SER SEQRES 20 A 585 GLU GLY VAL SER LEU PRO LEU GLY ASN THR LYS ASP PHE SEQRES 21 A 585 ILE ILE SER PHE ASP LEU LYS PHE THR SER ASN GLY SER SEQRES 22 A 585 VAL SER VAL ILE LEU GLU THR THR GLU LYS GLY PRO PRO SEQRES 23 A 585 PHE VAL ILE HIS TYR VAL THR THR THR GLN LEU ILE LEU SEQRES 24 A 585 LEU LYS ASP ARG ASP ILE THR TYR GLY ILE GLY PRO ARG SEQRES 25 A 585 THR THR TRP THR THR VAL THR ARG ASP LEU LEU THR ASP SEQRES 26 A 585 LEU ARG LYS GLY ILE GLY LEU SER ASN THR LYS ALA VAL SEQRES 27 A 585 LYS ALA THR LYS THR MET PRO ARG ARG VAL VAL LYS LEU SEQRES 28 A 585 VAL VAL HIS GLY THR GLY THR ILE ASP ASN ILE THR ILE SEQRES 29 A 585 SER THR THR SER HIS MET ALA ALA PHE TYR ALA ALA SER SEQRES 30 A 585 ASP TRP LEU VAL ARG ASN GLN ASP GLU ARG GLY GLY TRP SEQRES 31 A 585 PRO ILE MET VAL THR ARG LYS LEU GLY GLU GLY PHE ARG SEQRES 32 A 585 ALA LEU GLU PRO GLY TRP TYR SER ALA MET ALA GLN GLY SEQRES 33 A 585 GLN ALA MET SER THR LEU VAL ARG ALA TYR LEU MET THR SEQRES 34 A 585 LYS ASP ASP ARG TYR LEU LYS ALA ALA LEU ARG ALA THR SEQRES 35 A 585 GLY PRO PHE LYS LEU PRO SER GLU GLN HIS GLY VAL LYS SEQRES 36 A 585 ALA VAL PHE MET ASN LYS TYR ASP TRP TYR GLU GLU TYR SEQRES 37 A 585 PRO THR ILE PRO SER SER PHE VAL LEU ASN GLY PHE ILE SEQRES 38 A 585 TYR SER LEU ILE GLY LEU PHE ASP LEU ALA GLN THR ALA SEQRES 39 A 585 GLY GLU LYS LEU GLY ARG ASP ALA GLY GLN LEU TYR SER SEQRES 40 A 585 LYS GLY MET GLU SER LEU LYS VAL MET LEU PRO LEU TYR SEQRES 41 A 585 ASP THR GLY SER GLY THR ILE TYR ASP LEU ARG HIS PHE SEQRES 42 A 585 ILE LEU GLY THR ALA PRO ASN LEU ALA ARG TRP ASP TYR SEQRES 43 A 585 HIS THR THR HIS ILE ASN GLN LEU GLN LEU LEU GLY THR SEQRES 44 A 585 ILE ASP ASN SER PRO ILE PHE ARG ASP SER VAL LYS ARG SEQRES 45 A 585 TRP LYS SER TYR LEU LYS GLY GLY ARG ALA LYS HIS ASN SEQRES 1 B 585 MET ARG CYS LEU ALA ALA GLY VAL HIS TYR LYS THR LEU SEQRES 2 B 585 ILE VAL ILE CYS ALA LEU LEU SER LEU LEU THR VAL LEU SEQRES 3 B 585 LEU TRP ASN LYS CYS THR SER GLU LYS ALA LEU ARG PHE SEQRES 4 B 585 LEU PRO GLN HIS PRO GLN PRO PRO PRO SER PRO LYS ILE SEQRES 5 B 585 ASP SER HIS PRO GLN GLN PRO GLN PRO PRO GLU PRO PRO SEQRES 6 B 585 PRO VAL VAL GLY GLY VAL ARG TYR GLU GLU ILE ASP CYS SEQRES 7 B 585 LEU ILE ASN ASP ASP ALA THR ILE LYS GLY ARG ARG GLU SEQRES 8 B 585 GLY SER GLU VAL TYR MET PRO PHE SER TRP MET GLU LYS SEQRES 9 B 585 TYR PHE GLU VAL TYR GLY LYS VAL VAL GLN TYR ASP GLY SEQRES 10 B 585 TYR ASP ARG PHE GLU PHE SER HIS SER TYR SER LYS VAL SEQRES 11 B 585 TYR ALA GLN ARG GLU GLN TYR HIS PRO ASN GLY VAL PHE SEQRES 12 B 585 MET SER PHE GLU GLY TYR ASN VAL GLU VAL ARG ASP ARG SEQRES 13 B 585 VAL LYS CYS ILE SER GLY VAL GLU GLY VAL PRO LEU SER SEQRES 14 B 585 THR GLN TRP GLY PRO GLN GLY TYR PHE TYR ALA ILE GLN SEQRES 15 B 585 ILE ALA GLN TYR GLY LEU SER HIS TYR SER LYS ASN LEU SEQRES 16 B 585 THR GLU ARG PRO PRO HIS VAL GLU VAL TYR ASP THR ALA SEQRES 17 B 585 GLU GLU ARG ASP SER ARG SER SER ALA TRP THR VAL PRO SEQRES 18 B 585 LYS GLY CYS SER LEU THR ARG VAL TYR ASP LYS THR ARG SEQRES 19 B 585 ALA THR SER VAL ARG GLU PHE SER ALA PRO GLU ASN SER SEQRES 20 B 585 GLU GLY VAL SER LEU PRO LEU GLY ASN THR LYS ASP PHE SEQRES 21 B 585 ILE ILE SER PHE ASP LEU LYS PHE THR SER ASN GLY SER SEQRES 22 B 585 VAL SER VAL ILE LEU GLU THR THR GLU LYS GLY PRO PRO SEQRES 23 B 585 PHE VAL ILE HIS TYR VAL THR THR THR GLN LEU ILE LEU SEQRES 24 B 585 LEU LYS ASP ARG ASP ILE THR TYR GLY ILE GLY PRO ARG SEQRES 25 B 585 THR THR TRP THR THR VAL THR ARG ASP LEU LEU THR ASP SEQRES 26 B 585 LEU ARG LYS GLY ILE GLY LEU SER ASN THR LYS ALA VAL SEQRES 27 B 585 LYS ALA THR LYS THR MET PRO ARG ARG VAL VAL LYS LEU SEQRES 28 B 585 VAL VAL HIS GLY THR GLY THR ILE ASP ASN ILE THR ILE SEQRES 29 B 585 SER THR THR SER HIS MET ALA ALA PHE TYR ALA ALA SER SEQRES 30 B 585 ASP TRP LEU VAL ARG ASN GLN ASP GLU ARG GLY GLY TRP SEQRES 31 B 585 PRO ILE MET VAL THR ARG LYS LEU GLY GLU GLY PHE ARG SEQRES 32 B 585 ALA LEU GLU PRO GLY TRP TYR SER ALA MET ALA GLN GLY SEQRES 33 B 585 GLN ALA MET SER THR LEU VAL ARG ALA TYR LEU MET THR SEQRES 34 B 585 LYS ASP ASP ARG TYR LEU LYS ALA ALA LEU ARG ALA THR SEQRES 35 B 585 GLY PRO PHE LYS LEU PRO SER GLU GLN HIS GLY VAL LYS SEQRES 36 B 585 ALA VAL PHE MET ASN LYS TYR ASP TRP TYR GLU GLU TYR SEQRES 37 B 585 PRO THR ILE PRO SER SER PHE VAL LEU ASN GLY PHE ILE SEQRES 38 B 585 TYR SER LEU ILE GLY LEU PHE ASP LEU ALA GLN THR ALA SEQRES 39 B 585 GLY GLU LYS LEU GLY ARG ASP ALA GLY GLN LEU TYR SER SEQRES 40 B 585 LYS GLY MET GLU SER LEU LYS VAL MET LEU PRO LEU TYR SEQRES 41 B 585 ASP THR GLY SER GLY THR ILE TYR ASP LEU ARG HIS PHE SEQRES 42 B 585 ILE LEU GLY THR ALA PRO ASN LEU ALA ARG TRP ASP TYR SEQRES 43 B 585 HIS THR THR HIS ILE ASN GLN LEU GLN LEU LEU GLY THR SEQRES 44 B 585 ILE ASP ASN SER PRO ILE PHE ARG ASP SER VAL LYS ARG SEQRES 45 B 585 TRP LYS SER TYR LEU LYS GLY GLY ARG ALA LYS HIS ASN HET SGN C 1 20 HET IDS C 2 16 HET SGN C 3 19 HET IDS C 4 16 HET SGN C 5 19 HET UAP C 6 15 HET SGN D 1 20 HET IDS D 2 16 HET SGN D 3 19 HET IDS D 4 16 HET SGN D 5 19 HET UAP D 6 15 HETNAM SGN 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE HETNAM IDS 2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID HETNAM UAP 4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENOPYRANURONIC HETNAM 2 UAP ACID HETSYN SGN N,O6-DISULFO-GLUCOSAMINE; 6-O-SULFO-N-SULFO-ALPHA-D- HETSYN 2 SGN GLUCOSAMINE; 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D- HETSYN 3 SGN GLUCOSE; 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-D-GLUCOSE; HETSYN 4 SGN 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-GLUCOSE HETSYN IDS O2-SULFO-GLUCURONIC ACID; 2-O-SULFO-ALPHA-L-IDURONIC HETSYN 2 IDS ACID; 2-O-SULFO-L-IDURONIC ACID; 2-O-SULFO-IDURONIC HETSYN 3 IDS ACID HETSYN UAP 4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENURONIC ACID; 4- HETSYN 2 UAP DEOXY-2-O-SULFO-L-THREO-HEX-4-ENURONIC ACID; 4-DEOXY- HETSYN 3 UAP 2-O-SULFO-THREO-HEX-4-ENURONIC ACID FORMUL 3 SGN 6(C6 H13 N O11 S2) FORMUL 3 IDS 4(C6 H10 O10 S) FORMUL 3 UAP 2(C6 H8 O9 S) FORMUL 5 HOH *813(H2 O) HELIX 1 1 PHE A 99 GLU A 107 1 9 HELIX 2 2 SER A 145 TYR A 149 5 5 HELIX 3 3 TYR A 179 GLU A 197 1 19 HELIX 4 4 ASP A 212 SER A 216 5 5 HELIX 5 5 LEU A 322 GLY A 331 1 10 HELIX 6 6 SER A 368 GLN A 384 1 17 HELIX 7 7 SER A 411 LYS A 430 1 20 HELIX 8 8 ASP A 431 ALA A 441 1 11 HELIX 9 9 THR A 442 LEU A 447 5 6 HELIX 10 10 PRO A 448 HIS A 452 5 5 HELIX 11 11 VAL A 476 GLY A 499 1 24 HELIX 12 12 GLY A 499 LEU A 517 1 19 HELIX 13 13 PRO A 518 ASP A 521 5 4 HELIX 14 14 LEU A 530 GLY A 536 1 7 HELIX 15 15 ARG A 543 THR A 559 1 17 HELIX 16 16 SER A 563 LEU A 577 1 15 HELIX 17 17 PHE B 99 GLU B 107 1 9 HELIX 18 18 SER B 145 TYR B 149 5 5 HELIX 19 19 TYR B 179 GLU B 197 1 19 HELIX 20 20 ASP B 212 SER B 216 5 5 HELIX 21 21 LEU B 322 GLY B 331 1 10 HELIX 22 22 SER B 368 GLN B 384 1 17 HELIX 23 23 SER B 411 LYS B 430 1 20 HELIX 24 24 ASP B 431 ALA B 441 1 11 HELIX 25 25 THR B 442 LEU B 447 5 6 HELIX 26 26 PRO B 448 HIS B 452 5 5 HELIX 27 27 MET B 459 LYS B 461 5 3 HELIX 28 28 VAL B 476 GLY B 499 1 24 HELIX 29 29 GLY B 499 LEU B 517 1 19 HELIX 30 30 PRO B 518 ASP B 521 5 4 HELIX 31 31 LEU B 530 GLY B 536 1 7 HELIX 32 32 ARG B 543 THR B 559 1 17 HELIX 33 33 SER B 563 LYS B 578 1 16 SHEET 1 A10 TYR A 109 VAL A 113 0 SHEET 2 A10 ARG A 120 SER A 124 -1 O SER A 124 N TYR A 109 SHEET 3 A10 TYR B 73 ILE B 80 1 O LEU B 79 N PHE A 123 SHEET 4 A10 ALA B 84 GLU B 91 -1 O ILE B 86 N CYS B 78 SHEET 5 A10 GLU B 94 PRO B 98 -1 O TYR B 96 N ARG B 89 SHEET 6 A10 GLU A 94 PRO A 98 -1 N MET A 97 O MET B 97 SHEET 7 A10 ALA A 84 GLU A 91 -1 N ARG A 89 O TYR A 96 SHEET 8 A10 GLU A 74 ILE A 80 -1 N CYS A 78 O ILE A 86 SHEET 9 A10 ASP B 119 SER B 124 1 O PHE B 123 N LEU A 79 SHEET 10 A10 TYR B 109 GLN B 114 -1 N VAL B 113 O ARG B 120 SHEET 1 B 2 VAL A 157 ILE A 160 0 SHEET 2 B 2 PRO A 167 SER A 169 -1 O LEU A 168 N CYS A 159 SHEET 1 C 4 VAL A 202 VAL A 204 0 SHEET 2 C 4 PRO A 345 SER A 365 -1 O ILE A 364 N GLU A 203 SHEET 3 C 4 ILE A 261 PHE A 268 -1 N ASP A 265 O ASP A 360 SHEET 4 C 4 THR A 316 ASP A 321 -1 O ARG A 320 N ILE A 262 SHEET 1 D 4 SER A 225 ASP A 231 0 SHEET 2 D 4 THR A 236 ALA A 243 -1 O GLU A 240 N THR A 227 SHEET 3 D 4 PRO A 345 SER A 365 -1 O GLY A 355 N ALA A 243 SHEET 4 D 4 VAL A 202 VAL A 204 -1 N GLU A 203 O ILE A 364 SHEET 1 E 6 VAL A 250 ASN A 256 0 SHEET 2 E 6 PRO A 345 SER A 365 -1 O VAL A 348 N ASN A 256 SHEET 3 E 6 SER A 273 THR A 280 -1 N GLU A 279 O ARG A 346 SHEET 4 E 6 PHE A 287 VAL A 292 -1 O PHE A 287 N LEU A 278 SHEET 5 E 6 ASP A 304 GLY A 308 1 O ILE A 305 N HIS A 290 SHEET 6 E 6 LEU A 299 LYS A 301 -1 N LEU A 299 O THR A 306 SHEET 1 F 2 LYS A 455 PHE A 458 0 SHEET 2 F 2 TYR A 462 TYR A 465 -1 O TYR A 462 N PHE A 458 SHEET 1 G 2 VAL B 157 ILE B 160 0 SHEET 2 G 2 PRO B 167 SER B 169 -1 O LEU B 168 N CYS B 159 SHEET 1 H 4 VAL B 202 VAL B 204 0 SHEET 2 H 4 PRO B 345 SER B 365 -1 O ILE B 364 N GLU B 203 SHEET 3 H 4 ILE B 261 PHE B 268 -1 N ASP B 265 O ASP B 360 SHEET 4 H 4 THR B 316 ASP B 321 -1 O ARG B 320 N ILE B 262 SHEET 1 I 4 SER B 225 ASP B 231 0 SHEET 2 I 4 THR B 236 ALA B 243 -1 O GLU B 240 N THR B 227 SHEET 3 I 4 PRO B 345 SER B 365 -1 O GLY B 355 N ALA B 243 SHEET 4 I 4 VAL B 202 VAL B 204 -1 N GLU B 203 O ILE B 364 SHEET 1 J 6 VAL B 250 ASN B 256 0 SHEET 2 J 6 PRO B 345 SER B 365 -1 O VAL B 348 N ASN B 256 SHEET 3 J 6 SER B 273 THR B 280 -1 N SER B 275 O VAL B 352 SHEET 4 J 6 PHE B 287 VAL B 292 -1 O PHE B 287 N LEU B 278 SHEET 5 J 6 ASP B 304 GLY B 308 1 O ILE B 305 N HIS B 290 SHEET 6 J 6 LEU B 299 LYS B 301 -1 N LYS B 301 O ASP B 304 SHEET 1 K 2 LYS B 455 PHE B 458 0 SHEET 2 K 2 TYR B 462 TYR B 465 -1 O TYR B 462 N PHE B 458 LINK O4 SGN C 1 C1 IDS C 2 1555 1555 1.44 LINK O4 IDS C 2 C1 SGN C 3 1555 1555 1.39 LINK O4 SGN C 3 C1 IDS C 4 1555 1555 1.43 LINK O4 IDS C 4 C1 SGN C 5 1555 1555 1.40 LINK O4 SGN C 5 C1 UAP C 6 1555 1555 1.41 LINK O4 SGN D 1 C1 IDS D 2 1555 1555 1.44 LINK O4 IDS D 2 C1 SGN D 3 1555 1555 1.41 LINK O4 SGN D 3 C1 IDS D 4 1555 1555 1.43 LINK O4 IDS D 4 C1 SGN D 5 1555 1555 1.39 LINK O4 SGN D 5 C1 UAP D 6 1555 1555 1.41 CISPEP 1 ILE A 471 PRO A 472 0 -2.45 CISPEP 2 ILE B 471 PRO B 472 0 -4.46 CRYST1 152.606 200.982 46.561 90.00 90.00 90.00 P 21 21 2 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 0.006553 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004976 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021477 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.028410 0.999298 0.024416 -70.74078 1 MTRIX2 2 0.999556 -0.028618 0.008241 72.61227 1 MTRIX3 2 0.008934 0.024171 -0.999668 7.14761 1