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- PDB-4pw2: Crystal structure of D-glucuronyl C5 epimerase -

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Basic information

Entry
Database: PDB / ID: 4pw2
TitleCrystal structure of D-glucuronyl C5 epimerase
ComponentsD-glucuronyl C5 epimerase B
KeywordsISOMERASE / epimerization enzyme / multiple domain structure / Heparan sulfate C5-epimerase / heparin / heparan sulfate
Function / homology
Function and homology information


heparosan-N-sulfate-glucuronate 5-epimerase / heparosan-N-sulfate-glucuronate 5-epimerase activity / heparin biosynthetic process / heparan sulfate proteoglycan biosynthetic process / Golgi membrane / Golgi apparatus / identical protein binding / metal ion binding
Similarity search - Function
D-glucuronyl C5-epimerase, C-terminal / D-glucuronyl C5-epimerase / D-glucuronyl C5-epimerase C-terminus / D-glucuronyl C5-epimerase, beta-sandwich domain
Similarity search - Domain/homology
CITRIC ACID / D-glucuronyl C5-epimerase B / D-glucuronyl C5-epimerase B
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKe, J. / Qin, Y. / Gu, X. / Brunzelle, J.S. / Xu, H.E. / Ding, K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Functional Study of d-Glucuronyl C5-epimerase.
Authors: Qin, Y. / Ke, J. / Gu, X. / Fang, J. / Wang, W. / Cong, Q. / Li, J. / Tan, J. / Brunzelle, J.S. / Zhang, C. / Jiang, Y. / Melcher, K. / Li, J.P. / Xu, H.E. / Ding, K.
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-glucuronyl C5 epimerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3282
Polymers66,1361
Non-polymers1921
Water12,322684
1
A: D-glucuronyl C5 epimerase B
hetero molecules

A: D-glucuronyl C5 epimerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,6574
Polymers132,2722
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6980 Å2
ΔGint-23 kcal/mol
Surface area44790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.379, 66.379, 337.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-960-

HOH

21A-1384-

HOH

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Components

#1: Protein D-glucuronyl C5 epimerase B


Mass: 66136.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: D-glucuronyl C5-epimerase, glce, glceb / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6TS32, UniProt: F1QR43*PLUS, heparosan-N-sulfate-glucuronate 5-epimerase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 684 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 16% w/v PEG 3,350, 0.1 M sodium citrate tribasic dihydrate pH 5.6, and 2% v/v Tacsimate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 15, 2013
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 61140 / Num. obs: 61140 / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 14.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 14.7 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 3.2 / Num. unique all: 8707 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→47.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.829 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24424 3094 5.1 %RANDOM
Rwork0.21019 ---
all0.21189 57978 --
obs0.21189 57920 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.239 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å20 Å2
2--1.42 Å20 Å2
3----2.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 13 684 4783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194202
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.9525696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5885508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78522.917192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94515704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4661531
X-RAY DIFFRACTIONr_chiral_restr0.0770.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213202
X-RAY DIFFRACTIONr_mcbond_it1.3353.3022038
X-RAY DIFFRACTIONr_mcangle_it2.2294.9422544
X-RAY DIFFRACTIONr_scbond_it1.6823.5372164
X-RAY DIFFRACTIONr_long_range_B_refined6.00632.01118944
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 234 -
Rwork0.295 4160 -
obs--99.82 %

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