7R1N | pdb_00007r1n

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

PDB DOI: https://doi.org/10.2210/pdb7R1N/pdb

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

Deposited: 2022-02-03 Released: 2023-02-15
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: 2.07 Å
R-Value Free:
0.271 (Depositor), 0.270 (DCC)
R-Value Work:
0.210 (Depositor), 0.203 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7R1N

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: 87.18 kDa
Atom Count: 5,772
Modeled Residue Count: 736
Deposited Residue Count: 828
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 [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain R [auth DDD] SDF format, chain P [auth CCC] SDF format, chain L [auth BBB] SDF format, chain E [auth AAA] MOL2 format, chain R [auth DDD] MOL2 format, chain P [auth CCC] MOL2 format, chain L [auth BBB] MOL2 format, chain E [auth AAA] mmCIF format, chain R [auth DDD] mmCIF format, chain P [auth CCC] mmCIF format, chain L [auth BBB] mmCIF format, chain E [auth AAA]	E [auth AAA], L [auth BBB], P [auth CCC], R [auth DDD]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain L [auth BBB] Focus chain P [auth CCC] Focus chain R [auth DDD] Interactions & Density Focus chain E [auth AAA] Focus chain L [auth BBB] Focus chain P [auth CCC] Focus chain R [auth DDD]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth BBB] SDF format, chain I [auth AAA] SDF format, chain G [auth AAA] SDF format, chain F [auth AAA] MOL2 format, chain M [auth BBB] MOL2 format, chain I [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain M [auth BBB] mmCIF format, chain I [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA], G [auth AAA], I [auth AAA], M [auth BBB]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain I [auth AAA] Focus chain M [auth BBB] Interactions & Density Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain I [auth AAA] Focus chain M [auth BBB]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth DDD] SDF format, chain H [auth AAA] MOL2 format, chain S [auth DDD] MOL2 format, chain H [auth AAA] mmCIF format, chain S [auth DDD] mmCIF format, chain H [auth AAA]	H [auth AAA], S [auth DDD]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Focus chain S [auth DDD] Interactions & Density Focus chain H [auth AAA] Focus chain S [auth DDD]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth BBB] SDF format, chain J [auth AAA] MOL2 format, chain N [auth BBB] MOL2 format, chain J [auth AAA] mmCIF format, chain N [auth BBB] mmCIF format, chain J [auth AAA]	J [auth AAA], N [auth BBB]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth AAA] Focus chain N [auth BBB] Interactions & Density Focus chain J [auth AAA] Focus chain N [auth BBB]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain T [auth DDD] SDF format, chain Q [auth CCC] SDF format, chain O [auth BBB] SDF format, chain K [auth AAA] MOL2 format, chain T [auth DDD] MOL2 format, chain Q [auth CCC] MOL2 format, chain O [auth BBB] MOL2 format, chain K [auth AAA] mmCIF format, chain T [auth DDD] mmCIF format, chain Q [auth CCC] mmCIF format, chain O [auth BBB] mmCIF format, chain K [auth AAA]	K [auth AAA], O [auth BBB], Q [auth CCC], T [auth DDD]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth AAA] Focus chain O [auth BBB] Focus chain Q [auth CCC] Focus chain T [auth DDD] Interactions & Density Focus chain K [auth AAA] Focus chain O [auth BBB] Focus chain Q [auth CCC] Focus chain T [auth DDD]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.271 (Depositor), 0.270 (DCC)
R-Value Work: 0.210 (Depositor), 0.203 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.65	α = 90
b = 101.14	β = 90
c = 107	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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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-15

Deposition Author(s):

Fontes, C.M.G.A.

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

Revision History (Full details and data files)

Version 1.0: 2023-02-15
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

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