2RGM

Rice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase

PDB DOI: https://doi.org/10.2210/pdb2RGM/pdb

Classification: HYDROLASE
Organism(s): Oryza sativa Japonica Group
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-10-04 Released: 2008-02-12
Deposition Author(s): Chuenchor, W., Ketudat Cairns, J.R., Pengthaisong, S., Robinson, R.C., Yuvaniyama, J., Chen, C.-J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.197
R-Value Work: 0.171
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 110.65 kDa
Atom Count: 9,023
Modelled Residue Count: 942
Deposited Residue Count: 962
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A, B	481	Oryza sativa Japonica Group	Mutation(s): 0 Gene Names: Os3bglu7 EC: 3.2.1.21
UniProt
Find proteins for Q75I93 (Oryza sativa subsp. japonica) Explore Q75I93 Go to UniProtKB: Q75I93
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q75I93
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	F [auth A], J [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
G2F Query on G2F Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	2-deoxy-2-fluoro-alpha-D-glucopyranose C₆ H₁₁ F O₅ ZCXUVYAZINUVJD-UKFBFLRUSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B]	G [auth A], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.197
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.287	α = 90
b = 101.286	β = 90
c = 127.253	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-02-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-02-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary

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2RGM

Rice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)