3WKG

Crystal structure of cellobiose 2-epimerase in complex with glucosylmannose

PDB DOI: https://doi.org/10.2210/pdb3WKG/pdb

Classification: ISOMERASE
Organism(s): Rhodothermus marinus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-10-21 Released: 2013-12-25
Deposition Author(s): Fujiwara, T., Saburi, W., Tanaka, I., Yao, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.194
R-Value Work: 0.167
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 47.93 kDa
Atom Count: 3,985
Modelled Residue Count: 410
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiose 2-epimerase	A	412	Rhodothermus marinus	Mutation(s): 0 Gene Names: ce EC: 5.1.3.11
UniProt
Find proteins for F8WRK9 (Rhodothermus marinus) Explore F8WRK9 Go to UniProtKB: F8WRK9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F8WRK9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-mannopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G76414HJ GlyCosmos: G76414HJ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.194
R-Value Work: 0.167
R-Value Observed: 0.168
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.893	α = 90
b = 87.691	β = 90
c = 94.191	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	model building
PHENIX	refinement
XDS	data reduction
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-12-25
Type: Initial release
Version 1.1: 2014-01-29
Changes: Database references
Version 1.2: 2014-02-26
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

3WKG

Crystal structure of cellobiose 2-epimerase in complex with glucosylmannose

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)