9VOO | pdb_00009voo

Engineered endo-1,3-beta-glucanase from Cellulosimicrobium cellulans crystallized at pH 6.2, CcGluECDMH1-E120Q

PDB DOI: https://doi.org/10.2210/pdb9VOO/pdb

Classification: HYDROLASE
Organism(s): Cellulosimicrobium cellulans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-07-01 Released: 2026-07-08
Deposition Author(s): Zhang, X.J., Li, T., Yin, H.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.203 (Depositor), 0.216 (DCC)
R-Value Work:
0.161 (Depositor), 0.172 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9VOO

This is version 1.0 of the entry. See complete history.

Literature

Structure of CcGluECDMH1-E120Q in pH 6.3

Zhang, X.J., Li, T., Yin, H.

To be published.

Macromolecule Content

Total Structure Weight: 26.65 kDa
Atom Count: 1,966
Modeled Residue Count: 236
Deposited Residue Count: 242
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase	A	242	Cellulosimicrobium cellulans	Mutation(s): 1 Gene Names: Ccel01_18180
UniProt
Find proteins for A0AAV5P7L0 (Cellulosimicrobium cellulans) Explore A0AAV5P7L0 Go to UniProtKB: A0AAV5P7L0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAV5P7L0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.76 Å
R-Value Free: 0.203 (Depositor), 0.216 (DCC)
R-Value Work: 0.161 (Depositor), 0.172 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.821	α = 90
b = 73.821	β = 90
c = 62.59	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
MOLREP	phasing
PHENIX	refinement
autoPROC	data scaling
autoPROC	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	2023YFC2812200

Revision History (Full details and data files)

Version 1.0: 2026-07-08
Type: Initial release

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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.