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- PDB-3vw5: Crystal structure of sugar epimerase from ruminal bacterium -

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Basic information

Entry
Database: PDB / ID: 3vw5
TitleCrystal structure of sugar epimerase from ruminal bacterium
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 / cytoplasm
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
Cellobiose 2-epimerase / Cellobiose 2-epimerase
Similarity search - Component
Biological speciesRuminococcus albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFujiwara, T. / Saburi, W. / Tanaka, I. / Yao, M.
CitationJournal: Febs Lett. / Year: 2013
Title: Crystal structure of Ruminococcus albus cellobiose 2-epimerase: structural insights into epimerization of unmodified sugar
Authors: Fujiwara, T. / Saburi, W. / Inoue, S. / Mori, H. / Matsui, H. / Tanaka, I. / Yao, M.
History
DepositionAug 2, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Cellobiose 2-epimerase


Theoretical massNumber of molelcules
Total (without water)136,0883
Polymers136,0883
Non-polymers00
Water2,810156
1
A: Cellobiose 2-epimerase


Theoretical massNumber of molelcules
Total (without water)45,3631
Polymers45,3631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellobiose 2-epimerase


Theoretical massNumber of molelcules
Total (without water)45,3631
Polymers45,3631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cellobiose 2-epimerase


Theoretical massNumber of molelcules
Total (without water)45,3631
Polymers45,3631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.930, 100.880, 186.000
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: 45362.727 Da / Num. of mol.: 3 / Mutation: G38E, P138L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus albus (bacteria) / Strain: NE1 / Gene: CE / Plasmid: pET23A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A8CF79, UniProt: P0DKY4*PLUS, cellobiose epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.6M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2011 / Details: mirrors
RadiationMonochromator: the rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. obs: 57248 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 48.981 Å2 / Rmerge(I) obs: 0.0085 / Net I/σ(I): 12.14
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8838 / % possible all: 95.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(AutoMR: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
PHENIX(AutoMR: 1.7.1_743)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GT5

3gt5


Resolution: 2.6→39.127 Å / SU ML: 0.63 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Phase error: 21.82
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 2895 5.06 %RANDOM
Rwork0.1727 ---
obs0.1751 54296 98.53 %-
all-57191 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.384 Å2 / ksol: 0.427 e/Å3
Displacement parametersBiso mean: 4.47 Å2
Baniso -1Baniso -2Baniso -3
1-6.5115 Å2-0 Å20 Å2
2---9.0437 Å2-0 Å2
3---2.5322 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9588 0 0 156 9744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089825
X-RAY DIFFRACTIONf_angle_d1.10313281
X-RAY DIFFRACTIONf_dihedral_angle_d17.8643573
X-RAY DIFFRACTIONf_chiral_restr0.0871362
X-RAY DIFFRACTIONf_plane_restr0.0041719
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.6-2.64170.30931370.25752360236092
2.6417-2.68720.30231250.24792542254298
2.6872-2.73610.29291530.24052542254299
2.7361-2.78870.30071430.23492547254799
2.7887-2.84560.30911480.22072568256899
2.8456-2.90740.26881480.21282533253399
2.9074-2.97510.25711330.20632586258699
2.9751-3.04940.26691270.20382585258599
3.0494-3.13180.27431390.19652586258699
3.1318-3.2240.29141430.20532568256899
3.224-3.3280.25111310.18432578257899
3.328-3.44680.2071330.17212605260599
3.4468-3.58480.19771340.16232579257999
3.5848-3.74780.20681420.15692563256399
3.7478-3.94520.20611280.15722601260198
3.9452-4.19210.22321280.14922624262499
4.1921-4.51540.20711330.1372616261699
4.5154-4.96890.13881430.12422604260499
4.9689-5.68610.21451350.16142663266399
5.6861-7.15670.21671520.17892659265999
7.1567-39.13150.18181400.16652787278798

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