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- PDB-5zhb: Structure of Cellobiose 2-Epimerase from Bacillus thermoamylovora... -

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Basic information

Entry
Database: PDB / ID: 5zhb
TitleStructure of Cellobiose 2-Epimerase from Bacillus thermoamylovorans B4167
ComponentsCellobiose 2-epimeraseCellobiose epimerase
KeywordsISOMERASE / cellobiose 2-epimerase / epimerization / 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 (GlcNAc 2-epimerase) / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Cellobiose 2-epimerase
Similarity search - Component
Biological speciesBacillus thermoamylovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsFeng, Y.H. / Yang, R.J. / Andrew, J.F.
CitationJournal: To Be Published
Title: Structure of Cellobiose 2-Epimerase from Bacillus thermoamylovorans B4167
Authors: Feng, Y.H. / Yang, R.J. / Andrew, J.F.
History
DepositionMar 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellobiose 2-epimerase
B: Cellobiose 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,37814
Polymers92,6342
Non-polymers74512
Water0
1
A: Cellobiose 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7518
Polymers46,3171
Non-polymers4347
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellobiose 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6276
Polymers46,3171
Non-polymers3105
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.979, 52.336, 129.602
Angle α, β, γ (deg.)90.00, 129.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cellobiose 2-epimerase / Cellobiose epimerase / CE


Mass: 46316.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermoamylovorans (bacteria) / Gene: B4166_1736, B4167_1620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D0GHZ5, cellobiose epimerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2

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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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Trimethylamine-N-oxide, 0.1M Tris-HCl, pH8.5, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 83031 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.17 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.05 / Net I/σ(I): 15.72
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.11 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 5958 / CC1/2: 0.794 / Rrim(I) all: 0.729 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.85→34.22 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.74
RfactorNum. reflection% reflection
Rfree0.21 3915 5.11 %
Rwork0.1759 --
obs0.1776 76659 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→34.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 48 0 6446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096694
X-RAY DIFFRACTIONf_angle_d0.8859047
X-RAY DIFFRACTIONf_dihedral_angle_d2.6955368
X-RAY DIFFRACTIONf_chiral_restr0.054904
X-RAY DIFFRACTIONf_plane_restr0.0061160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87260.35171420.28442634X-RAY DIFFRACTION99
1.8726-1.89630.29651350.25992540X-RAY DIFFRACTION99
1.8963-1.92120.31121580.2542608X-RAY DIFFRACTION99
1.9212-1.94750.30481510.23722587X-RAY DIFFRACTION99
1.9475-1.97540.24121500.2182579X-RAY DIFFRACTION99
1.9754-2.00480.25771460.21022607X-RAY DIFFRACTION98
2.0048-2.03620.26981390.21272564X-RAY DIFFRACTION99
2.0362-2.06950.21911110.19382619X-RAY DIFFRACTION99
2.0695-2.10520.21671280.19182621X-RAY DIFFRACTION98
2.1052-2.14350.23271370.18712521X-RAY DIFFRACTION97
2.1435-2.18470.21471340.18632467X-RAY DIFFRACTION93
2.1847-2.22930.22121360.18282522X-RAY DIFFRACTION98
2.2293-2.27780.2471730.18742613X-RAY DIFFRACTION99
2.2778-2.33080.23291460.1872582X-RAY DIFFRACTION99
2.3308-2.3890.22541370.18122658X-RAY DIFFRACTION99
2.389-2.45360.1961410.17412595X-RAY DIFFRACTION99
2.4536-2.52580.20241300.17992614X-RAY DIFFRACTION99
2.5258-2.60730.21011390.17082625X-RAY DIFFRACTION99
2.6073-2.70040.22371370.16842619X-RAY DIFFRACTION99
2.7004-2.80850.23821300.18882519X-RAY DIFFRACTION95
2.8085-2.93630.22061450.18072587X-RAY DIFFRACTION98
2.9363-3.0910.22641420.18252638X-RAY DIFFRACTION99
3.091-3.28450.21481470.18082611X-RAY DIFFRACTION99
3.2845-3.53780.22681440.17452625X-RAY DIFFRACTION99
3.5378-3.89340.19171460.15982590X-RAY DIFFRACTION98
3.8934-4.45580.14751220.14362615X-RAY DIFFRACTION97
4.4558-5.60980.17521380.15142672X-RAY DIFFRACTION99
5.6098-34.2260.18111310.16932712X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 43.0507 Å / Origin y: 47.5571 Å / Origin z: 26.1511 Å
111213212223313233
T0.2017 Å20.0235 Å2-0.0338 Å2-0.2536 Å2-0.0003 Å2--0.1664 Å2
L1.7149 °2-0.5305 °2-0.5161 °2-0.4322 °20.1598 °2--0.5906 °2
S-0.0792 Å °-0.2851 Å °-0.0377 Å °0.0559 Å °0.1234 Å °0.0266 Å °0.0083 Å °0.0163 Å °-0.0442 Å °
Refinement TLS groupSelection details: all

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