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- PDB-3wki: Crystal structure of cellobiose 2-epimerase in complex with cello... -

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Basic information

Entry
Database: PDB / ID: 3wki
TitleCrystal structure of cellobiose 2-epimerase in complex with cellobiitol
ComponentsCellobiose 2-epimerase
KeywordsISOMERASE / (alpha/alpha)6 barrel fold / Epimerase / Carbohydrate/Sugar Binding / Epimerization
Function / homology
Function and homology information


cellobiose epimerase / cellobiose epimerase activity / carbohydrate metabolic process
Similarity search - Function
Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase/Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Cellobiose 2-epimerase
Similarity search - Component
Biological speciesRhodothermus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.191 Å
AuthorsFujiwara, T. / Saburi, W. / Tanaka, I. / Yao, M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Insights into the Epimerization of beta-1,4-Linked Oligosaccharides Catalyzed by Cellobiose 2-Epimerase, the Sole Enzyme Epimerizing Non-anomeric Hydroxyl Groups of Unmodified Sugars
Authors: Fujiwara, T. / Saburi, W. / Matsui, H. / Mori, H. / Yao, M.
History
DepositionOct 21, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Feb 26, 2014Group: 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Cellobiose 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9324
Polymers47,4591
Non-polymers4733
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.675, 87.216, 93.541
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cellobiose 2-epimerase / CE


Mass: 47459.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus (bacteria) / Strain: JCM9785 / Gene: ce / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: F8WRK9, cellobiose epimerase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-D-glucose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[o2122h][a2122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][<C6O5>]{[(1+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 1.79 Å3/Da / Density % sol: 31.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M sodium acetate buffer pH 4.5, 1.0M ammonium hydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 18, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 18054 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 14.6
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 7 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2775 / % possible all: 96.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(AutoMR: 1.7.1_743)model building
PHENIX(phenix.refine: dev_1389)refinement
XDSdata reduction
PHENIX(AutoMR: 1.7.1_743)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WKF

3wkf


Resolution: 2.191→38.068 Å / SU ML: 0.25 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 919 5.09 %RANDOM
Rwork0.1607 ---
obs0.1639 18049 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.191→38.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 29 231 3577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073443
X-RAY DIFFRACTIONf_angle_d1.0784684
X-RAY DIFFRACTIONf_dihedral_angle_d14.1991240
X-RAY DIFFRACTIONf_chiral_restr0.074484
X-RAY DIFFRACTIONf_plane_restr0.005613
LS refinement shellResolution: 2.191→2.3067 Å
RfactorNum. reflection% reflection
Rfree0.3037 126 -
Rwork0.2178 2293 -
obs--96 %

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