3NSX

The crystal structure of the The crystal structure of the D420A mutant of the alpha-glucosidase (FAMILY 31) from Ruminococcus obeum ATCC 29174

PDB DOI: https://doi.org/10.2210/pdb3NSX/pdb

Classification: HYDROLASE
Organism(s): Blautia obeum ATCC 29174
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-07-02 Released: 2010-07-21
Deposition Author(s): Tan, K., Tesar, C., Wilton, R., Keigher, L., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.179
R-Value Work: 0.153
R-Value Observed: 0.155

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of the The crystal structure of the D420A mutant of the alpha-glucosidase (FAMILY 31) from Ruminococcus obeum ATCC 29174

Tan, K., Tesar, C., Wilton, R., Keigher, L., Babnigg, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 155.18 kDa
Atom Count: 12,583
Modelled Residue Count: 1,332
Deposited Residue Count: 1,332
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-glucosidase	A, B	666	Blautia obeum ATCC 29174	Mutation(s): 1 Gene Names: RUMOBE_03919
UniProt
Find proteins for A5ZY13 (Blautia obeum ATCC 29174) Explore A5ZY13 Go to UniProtKB: A5ZY13
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5ZY13
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 C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B]	C [auth A], D [auth A], E [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.179
R-Value Work: 0.153
R-Value Observed: 0.155
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.827	α = 90
b = 120.021	β = 109.1
c = 88.247	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-07-21

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-07-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-06
Changes: Database references, Derived calculations
Version 1.3: 2023-09-06
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.