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- PDB-8wbu: The crystal structure of circular mannose with mutant H247F of th... -

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Basic information

Entry
Database: PDB / ID: 8wbu
TitleThe crystal structure of circular 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 / Cellobiose 2-epimerase
Similarity search - Component
Biological speciesCaldicellulosiruptor saccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)47,1644
Polymers46,6231
Non-polymers5403
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint4 kcal/mol
Surface area15510 Å2
Unit cell
Length a, b, c (Å)55.540, 75.350, 91.740
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-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.8 M NaCl, 0.1 M Tris-HCl pH 8.5, 32% PEG 3350

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Data collection

DiffractionMean temperature: 193 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: 1.7→50 Å / Num. obs: 42563 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.64
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 3127 / CC1/2: 0.678 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.851 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 2123 5 %
Rwork0.1683 --
obs0.17 42502 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→34.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 36 180 3505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063448
X-RAY DIFFRACTIONf_angle_d0.8294656
X-RAY DIFFRACTIONf_dihedral_angle_d2.562833
X-RAY DIFFRACTIONf_chiral_restr0.052485
X-RAY DIFFRACTIONf_plane_restr0.005585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73940.30081430.25262654X-RAY DIFFRACTION99
1.7394-1.78290.2751210.22842698X-RAY DIFFRACTION100
1.7829-1.83110.25331260.22772690X-RAY DIFFRACTION100
1.8311-1.8850.21731450.21352666X-RAY DIFFRACTION99
1.885-1.94590.22021510.19492624X-RAY DIFFRACTION98
1.9459-2.01540.21471480.18012674X-RAY DIFFRACTION100
2.0154-2.09610.18811310.17272704X-RAY DIFFRACTION99
2.0961-2.19150.20991620.16562677X-RAY DIFFRACTION99
2.1915-2.3070.20311630.16782638X-RAY DIFFRACTION98
2.307-2.45150.20671470.16062660X-RAY DIFFRACTION98
2.4515-2.64070.20521280.16542745X-RAY DIFFRACTION99
2.6407-2.90630.19881440.17612704X-RAY DIFFRACTION99
2.9063-3.32660.24481210.17152695X-RAY DIFFRACTION98
3.3266-4.19010.16211410.14192740X-RAY DIFFRACTION98
4.1901-34.8510.18151520.15392810X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 1.2909 Å / Origin y: -0.3951 Å / Origin z: -8.164 Å
111213212223313233
T0.1577 Å20.0012 Å20.001 Å2-0.1426 Å2-0.0029 Å2--0.1533 Å2
L0.9016 °20.0656 °20.0315 °2-0.7755 °2-0.1758 °2--0.7381 °2
S0.0363 Å °0.0076 Å °0.0469 Å °-0.0039 Å °-0.0338 Å °-0.0085 Å °-0.0281 Å °0.0269 Å °-0.0015 Å °
Refinement TLS groupSelection details: all

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