3W53 | pdb_00003w53

Crystal structure of psychrophilic beta-glucosidase BglU from Micrococcus antarcticus

PDB DOI: https://doi.org/10.2210/pdb3W53/pdb

Classification: HYDROLASE
Organism(s): Micrococcus antarcticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-01-18 Released: 2014-01-22
Deposition Author(s): Hou, Y.J., Miao, L.L., Li, D.F., Liu, Z.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.200 (Depositor), 0.192 (DCC)
R-Value Work:
0.161 (Depositor), 0.156 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Structural and biochemical identification of key factors responsible for cold adaptation of Micrococcus antarcticus beta-glucosidase BglU

Miao, L.L., Hou, Y.J., Fan, H.X., Qu, J., Qi, C., Liu, Y., Li, D.F., Liu, Z.P.

To be published.

Macromolecule Content

Total Structure Weight: 56.43 kDa
Atom Count: 4,156
Modeled Residue Count: 469
Deposited Residue Count: 506
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A	506	Micrococcus antarcticus	Mutation(s): 0 Gene Names: BglU EC: 3.2.1.21
UniProt
Find proteins for B9V8P5 (Micrococcus antarcticus) Explore B9V8P5 Go to UniProtKB: B9V8P5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9V8P5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.200 (Depositor), 0.192 (DCC)
R-Value Work: 0.161 (Depositor), 0.156 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.28	α = 90
b = 84.67	β = 90
c = 184.77	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASES	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-01-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-01-22
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.