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- PDB-9l8k: Rhodothermus marines cellobiose 2-epimerase RmCE in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9l8k
TitleRhodothermus marines cellobiose 2-epimerase RmCE in complex with mannobiitol
ComponentsCellobiose 2-epimerase
KeywordsISOMERASE / cellobiose 2-epimerase / mannobiitol / epimerization
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-MANNITOL / PHOSPHATE ION / Cellobiose 2-epimerase
Similarity search - Component
Biological speciesRhodothermus marinus JCM 9785 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSaburi, W. / Muto, H. / Jaito, N. / Kato, K. / Yu, J. / Yao, M. / Mori, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2025
Title: Biochemical and structural analysis of the mechanism for the catalysis and specificity of cellobiose 2-epimerase from Rhodothermus marinus.
Authors: Saburi, W. / Muto-Fukiya, H. / Jaito, N. / Kato, K. / Yu, J. / Yao, M. / Mori, H.
History
DepositionDec 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8795
Polymers47,3861
Non-polymers4934
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-12 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.842, 87.192, 93.713
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Cellobiose 2-epimerase / CE


Mass: 47386.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: H36P conflict: error in database
Source: (gene. exp.) Rhodothermus marinus JCM 9785 (bacteria)
Gene: ce / Production host: Escherichia coli (E. coli) / References: UniProt: F8WRK9, cellobiose epimerase
#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

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Non-polymers , 4 types, 246 molecules

#2: Chemical ChemComp-MTL / D-MANNITOL


Mass: 182.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10 mM mannobiitol, 48 mM NaCl, 100 mM sodium acetate buffer (pH 4.5), 1.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 38532 / % possible obs: 99.2 % / Redundancy: 6.68 % / CC1/2: 0.997 / Net I/σ(I): 11.15
Reflection shellResolution: 1.7→1.8 Å / Num. unique obs: 6093 / CC1/2: 0.749

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Processing

Software
NameVersionClassification
PHENIX1.13_2998: ???refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WKF

3wkf


Resolution: 1.7→46.856 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2014 1921 -
Rwork0.1653 --
obs0.1671 38514 99.93 %
Refinement stepCycle: LAST / Resolution: 1.7→46.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 29 243 3586

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