7WW4 | pdb_00007ww4

Crystal structure of multidomain beta-1,3(4)-glucanase

PDB DOI: https://doi.org/10.2210/pdb7WW4/pdb

Classification: HYDROLASE
Organism(s): Pedobacter sp.
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-02-12 Released: 2023-02-15
Deposition Author(s): Jiang, Z.Q., Ma, J.W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.285 (Depositor), 0.279 (DCC)
R-Value Work:
0.248 (Depositor)
R-Value Observed:
0.250 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7WW4

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

Literature

Crystal structure of multidomain beta-1,3(4)-glucanase

Jiang, Z.Q., Ma, J.W.

To be published.

Macromolecule Content

Total Structure Weight: 55.25 kDa
Atom Count: 3,818
Modeled Residue Count: 480
Deposited Residue Count: 480
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-1,3(4)-glucanase	A	480	Pedobacter sp.	Mutation(s): 0
UniProt
Find proteins for A0A1G7XNR7 (Pedobacter terrae) Explore A0A1G7XNR7 Go to UniProtKB: A0A1G7XNR7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1G7XNR7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		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: 2.23 Å
R-Value Free: 0.285 (Depositor), 0.279 (DCC)
R-Value Work: 0.248 (Depositor)
R-Value Observed: 0.250 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.94	α = 90
b = 120.94	β = 90
c = 70.05	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data scaling
PHENIX	model building
PHENIX	refinement

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-02-15
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

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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.