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- PDB-7d5g: Crystal structure of the CsCE with ligand to have a insight into ... -

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Basic information

Entry
Database: PDB / ID: 7d5g
TitleCrystal structure of the CsCE with ligand to have a insight into the catalytic mechanism
ComponentsCellobiose 2-epimerase
KeywordsPROTEIN BINDING / cellobiose 2-epimerase / ligand / epimerization / isomerization
Function / homologycellobiose epimerase / Cellobiose 2-epimerase / cellobiose epimerase activity / N-acylglucosamine 2-epimerase/Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / Cellobiose 2-epimerase
Function and homology information
Biological speciesCaldicellulosiruptor saccharolyticus DSM 8903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYang, R.J. / Feng, Y.H. / Andrew, J.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31771912 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction
Authors: Feng, Y. / Lyu, X. / Cong, Y. / Miao, T. / Fang, B. / Zhang, C. / Shen, Q. / Matthews, M. / Fisher, A.J. / Zhang, J.Z. / Zhang, L. / Yang, R.
History
DepositionSep 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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)46,9195
Polymers46,4701
Non-polymers4494
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.729, 90.729, 97.723
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

21A-735-

HOH

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Components

#1: Protein Cellobiose 2-epimerase / CE


Mass: 46469.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor saccharolyticus DSM 8903 (bacteria)
Strain: DSM 8903 / Gene: Csac_0294
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A4XGA6, cellobiose epimerase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.16 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5 / Details: Mgnesium chloride, Bis-HCl, PEG4000

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→66.49 Å / Num. obs: 54194 / % possible obs: 99.9 % / Redundancy: 6.48 % / Biso Wilson estimate: 18.73 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.182 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2756 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z4J

4z4j


Resolution: 1.6→66.49 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2016 2742 5.06 %
Rwork0.1661 51451 -
obs0.1678 54193 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.48 Å2 / Biso mean: 23.5491 Å2 / Biso min: 9.07 Å2
Refinement stepCycle: final / Resolution: 1.6→66.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3279 0 48 323 3650
Biso mean--41.09 34.64 -
Num. residues----389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.630.29281480.264125212669100
1.63-1.660.25021300.241425392669100
1.66-1.690.24961310.222925532684100
1.69-1.720.27791500.210824952645100
1.72-1.760.21751350.206725572692100
1.76-1.80.24961190.200325452664100
1.8-1.850.24691520.204625522704100
1.85-1.90.23471560.204425222678100
1.9-1.950.24421270.185825562683100
1.95-2.020.22551580.177325542712100
2.02-2.090.19481350.164825452680100
2.09-2.170.21021120.160125822694100
2.17-2.270.2091400.161925842724100
2.27-2.390.20181300.165325792709100
2.39-2.540.21041020.163626042706100
2.54-2.740.24331480.165925822730100
2.74-3.010.17251360.159625822718100
3.01-3.450.17091490.15812609275899
3.45-4.340.16351270.13512639276699
4.34-66.490.17631570.15132751290898

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