6R2J | pdb_00006r2j

Crystal Structure of Pseudomonas stutzeri endoglucanase Cel5A in complex with cellobiose

PDB DOI: https://doi.org/10.2210/pdb6R2J/pdb

Classification: HYDROLASE
Organism(s): Stutzerimonas stutzeri A1501
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-03-18 Released: 2020-01-29
Deposition Author(s): Dutoit, R., Delsaute, M., Berlemont, R., Van Elder, D., Galleni, M., Bauvois, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free:
0.224 (Depositor), 0.200 (DCC)
R-Value Work:
0.179 (Depositor), 0.179 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure determination of Pseudomonas stutzeri A1501 endoglucanase Cel5A: the search for a molecular basis for glycosynthesis in GH5_5 enzymes.

Dutoit, R., Delsaute, M., Collet, L., Vander Wauven, C., Van Elder, D., Berlemont, R., Richel, A., Galleni, M., Bauvois, C.

(2019) Acta Crystallogr D Struct Biol 75: 605-615

DOI: https://doi.org/10.1107/S2059798319007113

Macromolecule Content

Total Structure Weight: 150.04 kDa
Atom Count: 12,620
Modeled Residue Count: 1,310
Deposited Residue Count: 1,320
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase(Endo-1,4-beta-glucanase)protein	A, B, C, D	330	Stutzerimonas stutzeri A1501	Mutation(s): 0 Gene Names: PST_2494
UniProt
Find proteins for A4VME5 (Stutzerimonas stutzeri (strain A1501)) Explore A4VME5 Go to UniProtKB: A4VME5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4VME5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	E, F	2		N/A	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain H [auth B]	G [auth A], H [auth B], I [auth C], J [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005 Query on PRD_900005	E, F	beta-cellobiose	Oligosaccharide / Metabolism		Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.224 (Depositor), 0.200 (DCC)
R-Value Work: 0.179 (Depositor), 0.179 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.25	α = 90
b = 82.82	β = 91.97
c = 104.68	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-01-29
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary