4QK0 | pdb_00004qk0

Crystal structure of Ara127N-Se, a GH127 beta-L-arabinofuranosidase from Geobacillus Stearothermophilus T6

PDB DOI: https://doi.org/10.2210/pdb4QK0/pdb

Classification: HYDROLASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-05 Released: 2015-06-10
Deposition Author(s): Lansky, S., Salama, R., Dann, R., Shner, I., Manjasetty, B., Belrhali, H., Shoham, Y., Shoham, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.200 (Depositor), 0.206 (DCC)
R-Value Work:
0.157 (Depositor), 0.170 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Ara127N-Se, a GH127 beta-L-arabinofuranosidase from Geobacillus Stearothermophilus T6

Lansky, S., Salama, R., Dann, R., Shner, I., Manjasetty, B., Belrhali, H., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 301.05 kDa
Atom Count: 22,177
Modeled Residue Count: 2,540
Deposited Residue Count: 2,592
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH127 beta-L-arabinofuranoside	A, B, C, D	648	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: araN
UniProt
Find proteins for B3EYN9 (Geobacillus stearothermophilus) Explore B3EYN9 Go to UniProtKB: B3EYN9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3EYN9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.200 (Depositor), 0.206 (DCC)
R-Value Work: 0.157 (Depositor), 0.170 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.383	α = 90
b = 132.266	β = 113.06
c = 109.045	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-06-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-10
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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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.