5CZL | pdb_00005czl

Crystal structure of a novel GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

PDB DOI: https://doi.org/10.2210/pdb5CZL/pdb

Classification: HYDROLASE
Organism(s): Klebsiella ornithinolytica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-07-31 Released: 2016-08-03
Deposition Author(s): Scapin, S.M.N., Souza, F.H.M., Zanphorlin, L.M., Almeida, T.S., Sade, Y.B., Cardoso, A.M., Pinheiro, G.L., Murakami, M.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.247 (Depositor), 0.248 (DCC)
R-Value Work:
0.201 (Depositor), 0.209 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5CZL

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a novel GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

Scapin, S.M.N., Souza, F.H.M., Zanphorlin, L.M., Almeida, T., Pinheiro, G.L., Murakami, M.T.

To be published.

Macromolecule Content

Total Structure Weight: 38.3 kDa
Atom Count: 2,574
Modeled Residue Count: 315
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucanase	A	338	Klebsiella ornithinolytica	Mutation(s): 0 Gene Names: TE10_01090 EC: 3.2.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.247 (Depositor), 0.248 (DCC)
R-Value Work: 0.201 (Depositor), 0.209 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.424	α = 90
b = 76.374	β = 90
c = 95.663	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-08-03

Deposition Author(s):

Zanphorlin, L.M.

Revision History (Full details and data files)

Version 1.0: 2016-08-03
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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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.