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- PDB-4pxq: Crystal structure of D-glucuronyl C5-epimerase in complex with he... -

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Basic information

Entry
Database: PDB / ID: 4pxq
TitleCrystal structure of D-glucuronyl C5-epimerase in complex with heparin hexasaccharide
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
D-glucuronyl C5-epimerase B / D-glucuronyl C5-epimerase B
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKe, J. / Qin, Y. / Gu, X. / Tan, J. / 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 24, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)135,7374
Polymers132,2722
Non-polymers3,4652
Water14,646813
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint1 kcal/mol
Surface area44140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.606, 200.982, 46.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.02841, 0.999298, 0.024416), (0.999556, -0.028618, 0.008241), (0.008934, 0.024171, -0.999668)-70.74078, 72.61227, 7.14761

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Components

#1: Protein D-glucuronyl C5 epimerase B


Mass: 66136.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: glce, glceb, Hsepi / Plasmid: pSumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q6TS32, UniProt: F1QR43*PLUS, heparosan-N-sulfate-glucuronate 5-epimerase
#2: Polysaccharide 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1732.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,6,5/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a21eEA-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-3/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 813 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 16% w/v PEG 3,350, 0.1 M sodium citrate tribasic dehydrate pH 5.6, and 2% v/v Tacsimate pH 5.0., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 74069 / Num. obs: 74069 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.292 / Net I/σ(I): 9.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 2 / Num. unique all: 10687 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→45.43 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.117 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22177 3728 5 %RANDOM
Rwork0.19431 ---
all0.19568 70293 --
obs0.19568 70265 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.385 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å20 Å2
2--0.34 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8252 0 210 813 9275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198682
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.97911813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78151029
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84222.887388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.454151422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.511564
X-RAY DIFFRACTIONr_chiral_restr0.2060.21308
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216482
X-RAY DIFFRACTIONr_mcbond_it1.4412.7184122
X-RAY DIFFRACTIONr_mcangle_it2.4574.0735149
X-RAY DIFFRACTIONr_scbond_it1.9732.9974558
X-RAY DIFFRACTIONr_long_range_B_refined6.39125.64538297
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 278 -
Rwork0.314 5089 -
obs--99.96 %

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