2Y2W | pdb_00002y2w

Elucidation of the substrate specificity and protein structure of AbfB, a family 51 alpha-L-arabinofuranosidase from Bifidobacterium longum.

PDB DOI: https://doi.org/10.2210/pdb2Y2W/pdb

Classification: HYDROLASE
Organism(s): Bifidobacterium longum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-12-16 Released: 2011-12-28
Deposition Author(s): Lagaert, S., Schoepe, J., Delcour, J.A., Lavigne, R., Strelkov, S.V., Courtin, C.M., Mikkelsen, N.E., Sandgren, M., Volckaert, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.270 (Depositor), 0.267 (DCC)
R-Value Work:
0.220 (Depositor), 0.218 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Elucidation of the Substrate Specificity and Protein Structure of Abfb, a Family 51 Alpha-L- Arabinofuranosidase from Bifidobacterium Longum.

Lagaert, S., Schoepe, J., Delcour, J.A., Lavigne, R., Strelkov, S.V., Courtin, C.M., Mikkelsen, N.E., Sandgren, M., Volckaert, G.

To be published.

Macromolecule Content

Total Structure Weight: 375.73 kDa
Atom Count: 24,278
Modeled Residue Count: 3,064
Deposited Residue Count: 3,444
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARABINOFURANOSIDASE	A, B, C, D, E A, B, C, D, E, F	574	Bifidobacterium longum	Mutation(s): 0 EC: 3.2.1.55
UniProt
Find proteins for Q8G554 (Bifidobacterium longum (strain NCC 2705)) Explore Q8G554 Go to UniProtKB: Q8G554
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8G554
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.270 (Depositor), 0.267 (DCC)
R-Value Work: 0.220 (Depositor), 0.218 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.469	α = 90
b = 165.811	β = 90
c = 184.297	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-12-28

Deposition Author(s):

Mikkelsen, N.E.

Revision History (Full details and data files)

Version 1.0: 2011-12-28
Type: Initial release
Version 1.1: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Other, 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.