4QJY | pdb_00004qjy

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

PDB DOI: https://doi.org/10.2210/pdb4QJY/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: 2.29 Å
R-Value Free:
0.214 (Depositor), 0.217 (DCC)
R-Value Work:
0.150 (Depositor), 0.160 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of native Ara127N, 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: 149.77 kDa
Atom Count: 11,013
Modeled Residue Count: 1,274
Deposited Residue Count: 1,296
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH127 beta-L-arabinofuranosidase	A, B	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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.214 (Depositor), 0.217 (DCC)
R-Value Work: 0.150 (Depositor), 0.160 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.536	α = 90
b = 118.098	β = 90
c = 174.984	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

View Full Validation Report

View more in-depth experimental data

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, Structure summary