5AFE | pdb_00005afe

Medium Resolution structure of the C-terminal family 65 Carbohydrate Binding Module (CBM65B) of endoglucanase Cel5A from Eubacterium cellulosolvens with a bound xyloglucan heptasaccharide (XXXG)

PDB DOI: https://doi.org/10.2210/pdb5AFE/pdb

Classification: HYDROLASE
Organism(s): [Eubacterium] cellulosolvens
Mutation(s): No

Deposited: 2015-01-21 Released: 2015-02-04
Deposition Author(s): Venditto, I., Fontes, C.M.G.A., Gilbert, H.J., Najmudin, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.306 (Depositor), 0.267 (DCC)
R-Value Work:
0.249 (Depositor), 0.253 (DCC)
R-Value Observed:
0.251 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Understanding How Noncatalytic Carbohydrate Binding Modules Can Display Specificity for Xyloglucan

Luis, A.S., Venditto, I., Basle, A., Prates, J.A.M., Ferreira, L.M.A., Temple, M., Rogowski, A., Xue, J., Knox, J.P., Fontes, C.M.G.A., Gilbert, H.J., Najmudin, S.

To be published.

Macromolecule Content

Total Structure Weight: 17.21 kDa
Atom Count: 1,090
Modeled Residue Count: 124
Deposited Residue Count: 144
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE CEL5A	A	144	[Eubacterium] cellulosolvens	Mutation(s): 0 EC: 3.2.1.4
UniProt
Find proteins for Q3LHN3 (Eubacterium cellulosolvens) Explore Q3LHN3 Go to UniProtKB: Q3LHN3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3LHN3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	7		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G24181CY GlyCosmos: G24181CY

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.306 (Depositor), 0.267 (DCC)
R-Value Work: 0.249 (Depositor), 0.253 (DCC)
R-Value Observed: 0.251 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.96	α = 90
b = 58.96	β = 90
c = 117.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-02-04

Deposition Author(s):

Fontes, C.M.G.A.

Revision History (Full details and data files)

Version 1.0: 2015-02-04
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.