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

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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
UniProt
Find proteins for A0A7Z9CPV5 (Klebsiella terrigena) Explore A0A7Z9CPV5 Go to UniProtKB: A0A7Z9CPV5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7Z9CPV5
Sequence Annotations Expand
Reference Sequence

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 C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [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