3SCO

Crystal Structure of Rice BGlu1 E386G Mutant Complexed with alpha-Glucosyl Fluoride

PDB DOI: https://doi.org/10.2210/pdb3SCO/pdb

Classification: HYDROLASE
Organism(s): Oryza sativa Japonica Group
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-06-08 Released: 2012-02-15
Deposition Author(s): Pengthaisong, S., Withers, S.G., Kuaprasert, B., Ketudat Cairns, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.207
R-Value Work: 0.172
R-Value Observed: 0.174

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural investigation of the basis for cellooligosaccharide synthesis by rice BGlu1 glycosynthases

Pengthaisong, S., Withers, S.G., Kuaprasert, B., Ketudat Cairns, J.R.

To be published.

Macromolecule Content

Total Structure Weight: 110.51 kDa
Atom Count: 8,512
Modelled Residue Count: 944
Deposited Residue Count: 962
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase 7	A, B	481	Oryza sativa Japonica Group	Mutation(s): 1 Gene Names: BGLU1, BGLU7, LOC_Os03g49600, Os03g0703000, os3bglu7, OSJNBa0004L11.16 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 E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
GLF Query on GLF 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] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	G [auth A], K [auth B]	alpha-D-glucopyranosyl fluoride C₆ H₁₁ F O₅ ATMYEINZLWEOQU-DVKNGEFBSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
GOL Query on GOL 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] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.207
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.852	α = 90
b = 100.806	β = 90
c = 127.114	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-02-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-15
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-11-13
Changes: Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

3SCO

Crystal Structure of Rice BGlu1 E386G Mutant Complexed with alpha-Glucosyl Fluoride

Structural investigation of the basis for cellooligosaccharide synthesis by rice BGlu1 glycosynthases

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)