7R3T | pdb_00007r3t

Crystal structure of the Dimeric C-terminal Big_2-CBM56 domains from Paenibacillus illinoisensis (Bacillus circulans IAM1165) beta-1,3-glucanase H

PDB DOI: https://doi.org/10.2210/pdb7R3T/pdb

Classification: HYDROLASE
Organism(s): Paenibacillus illinoisensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-02-07 Released: 2023-02-22
Deposition Author(s): Najmudin, S., Venditto, I., Fontes, C.M.G.A., Bule, P.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia, European Communitys Seventh Framework Programme

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.296 (Depositor), 0.301 (DCC)
R-Value Work:
0.221 (Depositor), 0.223 (DCC)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structural and biochemical characterization of C-terminal Big_2-CBM56 domains of Paenibacillus illinoisensis IAM1165 beta-1,3-glucanase H and Paenibacillus sp CBM56

Najmudin, S., Venditto, I., Pires, V.R., Caseiro, C., Correia, M.A.S., Romao, M.J., Carvalho, A.L., Fontes, C.M.G.A., Bule, P.

To be published.

Macromolecule Content

Total Structure Weight: 43.57 kDa
Atom Count: 2,833
Modeled Residue Count: 367
Deposited Residue Count: 414
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-1,3-glucanase bglH	A, B	207	Paenibacillus illinoisensis	Mutation(s): 0 Gene Names: bglH, beta-1, 3-glucanase
UniProt
Find proteins for Q45095 (Niallia circulans) Explore Q45095 Go to UniProtKB: Q45095
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q45095
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
PG4 Query on PG4 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]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	G [auth B], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.296 (Depositor), 0.301 (DCC)
R-Value Work: 0.221 (Depositor), 0.223 (DCC)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.63	α = 90
b = 76.38	β = 90
c = 106.87	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-22

Deposition Author(s):

Fontes, C.M.G.A.

Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BIA-PRO/103980/2008
European Communitys Seventh Framework Programme	European Union	263916

Revision History (Full details and data files)

Version 1.0: 2023-02-22
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

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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.