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- PDB-5zig: The Structure of cellobiose 2-epimerase from Spirochaeta thermoph... -

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Basic information

Entry
Database: PDB / ID: 5zig
TitleThe Structure of cellobiose 2-epimerase from Spirochaeta thermophila DSM 6192
ComponentsCellobiose 2-epimerase
KeywordsISOMERASE / Cellobiose 2-epimerase / isomerization / epimerization / lactose / 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) / 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 speciesSpirochaeta thermophila DSM 6192 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsFeng, Y.H. / Yang, R.J. / Andrew, J.F.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Insight into the potential factors influencing the catalytic direction in cellobiose 2-epimerase by crystallization and mutagenesis.
Authors: Feng, Y. / Hua, X. / Shen, Q. / Matthews, M. / Zhang, Y. / Fisher, A.J. / Lyu, X. / Yang, R.
History
DepositionMar 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)184,1676
Polymers184,0424
Non-polymers1242
Water10,971609
1
A: Cellobiose 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0732
Polymers46,0111
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellobiose 2-epimerase


Theoretical massNumber of molelcules
Total (without water)46,0111
Polymers46,0111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cellobiose 2-epimerase


Theoretical massNumber of molelcules
Total (without water)46,0111
Polymers46,0111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cellobiose 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0732
Polymers46,0111
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.530, 205.164, 67.723
Angle α, β, γ (deg.)90.00, 104.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cellobiose 2-epimerase / CE


Mass: 46010.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirochaeta thermophila DSM 6192 (bacteria)
Strain: ATCC 49972 / DSM 6192 / RI 19.B1 / Gene: STHERM_c00950
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: E0RU15, cellobiose epimerase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ca Acetate, 0.1M Bis-Tris-HCl, pH8.5, 20% PEG 3350

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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 S 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: 2.05→102.6 Å / Num. obs: 96356 / % possible obs: 86.55 % / Observed criterion σ(I): -3 / Redundancy: 1.86 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.057 / Net I/σ(I): 12.94
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 1.77 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 6722 / CC1/2: 0.794 / Rrim(I) all: 0.52 / % possible all: 82.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.05→32.746 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.4 / Phase error: 29.67
RfactorNum. reflection% reflection
Rfree0.2669 4800 4.98 %
Rwork0.1955 --
obs0.199 96337 86.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→32.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12935 0 8 609 13552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813526
X-RAY DIFFRACTIONf_angle_d0.89818461
X-RAY DIFFRACTIONf_dihedral_angle_d2.74610706
X-RAY DIFFRACTIONf_chiral_restr0.051895
X-RAY DIFFRACTIONf_plane_restr0.0062402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07330.39051360.29842648X-RAY DIFFRACTION77
2.0733-2.09770.33151580.27243088X-RAY DIFFRACTION87
2.0977-2.12330.33161560.25723055X-RAY DIFFRACTION86
2.1233-2.15010.28781610.24123004X-RAY DIFFRACTION87
2.1501-2.17840.33561650.24273136X-RAY DIFFRACTION87
2.1784-2.20830.37551510.24222947X-RAY DIFFRACTION86
2.2083-2.23980.31051880.22913002X-RAY DIFFRACTION86
2.2398-2.27320.31331390.21833087X-RAY DIFFRACTION87
2.2732-2.30870.31451460.21283003X-RAY DIFFRACTION85
2.3087-2.34660.30471760.21073024X-RAY DIFFRACTION86
2.3466-2.3870.30941380.21452982X-RAY DIFFRACTION84
2.387-2.43040.2951420.21993055X-RAY DIFFRACTION86
2.4304-2.47720.29581580.22152794X-RAY DIFFRACTION81
2.4772-2.52770.29781550.21322913X-RAY DIFFRACTION83
2.5277-2.58260.3132000.21133175X-RAY DIFFRACTION91
2.5826-2.64270.27551680.21213173X-RAY DIFFRACTION91
2.6427-2.70870.30091720.19973252X-RAY DIFFRACTION91
2.7087-2.78190.31421840.19483168X-RAY DIFFRACTION92
2.7819-2.86380.26961510.20153208X-RAY DIFFRACTION90
2.8638-2.95610.28791910.20053176X-RAY DIFFRACTION90
2.9561-3.06170.27071390.20313136X-RAY DIFFRACTION88
3.0617-3.18420.31681410.20662990X-RAY DIFFRACTION85
3.1842-3.3290.29831540.20172921X-RAY DIFFRACTION83
3.329-3.50430.27071600.19283220X-RAY DIFFRACTION92
3.5043-3.72360.25771580.19013210X-RAY DIFFRACTION90
3.7236-4.01060.24641610.17073105X-RAY DIFFRACTION88
4.0106-4.41340.21831560.16253031X-RAY DIFFRACTION86
4.4134-5.050.20431640.15552861X-RAY DIFFRACTION81
5.05-6.35480.22111650.1873161X-RAY DIFFRACTION89
6.3548-32.750.19771670.16893012X-RAY DIFFRACTION84
Refinement TLS params.Method: refined / Origin x: 52.0563 Å / Origin y: 138.1451 Å / Origin z: 20.874 Å
111213212223313233
T0.1718 Å20.0225 Å2-0.0026 Å2-0.3666 Å2-0.0179 Å2--0.1977 Å2
L0.0963 °20.0202 °20.0268 °2-0.1604 °20.0004 °2--0.0844 °2
S-0.0102 Å °0.0114 Å °0.0143 Å °-0.0073 Å °0.0246 Å °-0.0002 Å °0.0087 Å °0.0059 Å °-0.0123 Å °
Refinement TLS groupSelection details: all

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