3NUK | pdb_00003nuk

THE CRYSTAL STRUCTURE OF THE W169Y mutant of ALPHA-GLUCOSIDASE (FAMILY 31) from RUMINOCOCCUS OBEUM ATCC 29174

PDB DOI: https://doi.org/10.2210/pdb3NUK/pdb

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

Deposited: 2010-07-07 Released: 2010-07-28
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: 2.06 Å
R-Value Free:
0.247 (Depositor), 0.250 (DCC)
R-Value Work:
0.195 (Depositor), 0.190 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

THE CRYSTAL STRUCTURE OF THE W169Y mutant of 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: 154.94 kDa
Atom Count: 11,119
Modeled Residue Count: 1,314
Deposited Residue Count: 1,332
Unique protein chains: 1

Macromolecules

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(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 EC: 3.2.1
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
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.247 (Depositor), 0.250 (DCC)
R-Value Work: 0.195 (Depositor), 0.190 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.798	α = 90
b = 125.531	β = 107.82
c = 88.296	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: 2010-07-28

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-07-28
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 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.