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- PDB-8wbv: The crystal structure of linear mannose with mutant H247F of the ... -

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Basic information

Entry
Database: PDB / ID: 8wbv
TitleThe crystal structure of linear mannose with mutant H247F of the cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus
ComponentsCellobiose 2-epimerase
KeywordsISOMERASE / cellobiose 2-epimerase / BIOSYNTHETIC PROTEIN
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) / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
beta-D-mannopyranose / D-mannose / Cellobiose 2-epimerase
Similarity search - Component
Biological speciesCaldicellulosiruptor saccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYang, R.J. / Feng, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32072150 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.H. / Zhang, L. / Yang, R.
History
DepositionSep 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _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)47,0464
Polymers46,6231
Non-polymers4223
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.790, 75.850, 97.010
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


Mass: 46623.121 Da / Num. of mol.: 1 / Mutation: H247F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor saccharolyticus (bacteria)
Strain: ATCC 43494 / DSM 8903 / Tp8T 6331 / Gene: Csac_0294 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4XGA6
#2: Sugar ChemComp-DNO / D-mannose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.8M NaCl,0.1Tris-HCI pH 8.5, 32% PEG3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 28308 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 3.27 % / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.35
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 2179 / CC1/2: 0.807 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.877 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 1420 5.02 %
Rwork0.1753 --
obs0.178 28274 92.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→29.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 28 128 3445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073434
X-RAY DIFFRACTIONf_angle_d0.8494632
X-RAY DIFFRACTIONf_dihedral_angle_d2.6692830
X-RAY DIFFRACTIONf_chiral_restr0.049484
X-RAY DIFFRACTIONf_plane_restr0.004581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01960.28491620.23862764X-RAY DIFFRACTION97
2.0196-2.10050.30291460.21672709X-RAY DIFFRACTION95
2.1005-2.19610.28091300.20152684X-RAY DIFFRACTION93
2.1961-2.31180.26141580.20262603X-RAY DIFFRACTION91
2.3118-2.45660.27711480.20322635X-RAY DIFFRACTION92
2.4566-2.64610.22271410.19592695X-RAY DIFFRACTION93
2.6461-2.91220.27821360.18552634X-RAY DIFFRACTION91
2.9122-3.33320.24411230.1692711X-RAY DIFFRACTION92
3.3332-4.19760.18031420.13792715X-RAY DIFFRACTION92
4.1976-29.8770.19121340.15522704X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: 27.0411 Å / Origin y: 1.0133 Å / Origin z: -9.3553 Å
111213212223313233
T0.1517 Å2-0.0007 Å2-0.0013 Å2-0.1148 Å2-0.0042 Å2--0.1477 Å2
L1.1453 °2-0.0272 °2-0.075 °2-0.9634 °20.2037 °2--1.1644 °2
S0.0347 Å °0.0299 Å °-0.0792 Å °-0.0277 Å °-0.0399 Å °0.0176 Å °0.0664 Å °-0.0415 Å °0.0045 Å °
Refinement TLS groupSelection details: all

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