3GNR

Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with covalently bound 2-deoxy-2-fluoroglucoside to the catalytic nucleophile E396

PDB DOI: https://doi.org/10.2210/pdb3GNR/pdb

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

Deposited: 2009-03-17 Released: 2009-07-21
Deposition Author(s): Seshadri, S., Akiyama, T., Opassiri, R., Kuaprasert, B., Cairns, J.R.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.185
R-Value Work: 0.162
R-Value Observed: 0.164

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: 55.68 kDa
Atom Count: 4,346
Modelled Residue Count: 478
Deposited Residue Count: 488
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Os03g0212800 protein	A	488	Oryza sativa Japonica Group	Mutation(s): 0 Gene Names: LOC_Os03g11420, Os03g0212800, Os3bglu6 locus ID: Os03g0212800 EC: 3.2.1.21 Membrane Entity: Yes
UniProt
Find proteins for Q8L7J2 (Oryza sativa subsp. japonica) Explore Q8L7J2 Go to UniProtKB: Q8L7J2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8L7J2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G2F Query on G2F Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-deoxy-2-fluoro-alpha-D-glucopyranose C₆ H₁₁ F O₅ ZCXUVYAZINUVJD-UKFBFLRUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.185
R-Value Work: 0.162
R-Value Observed: 0.164
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.679	α = 90
b = 90.591	β = 90
c = 101.883	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-07-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-07-21
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: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary

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3GNR

Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with covalently bound 2-deoxy-2-fluoroglucoside to the catalytic nucleophile E396

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)