3MI6 | pdb_00003mi6

Crystal structure of the alpha-galactosidase from Lactobacillus brevis, Northeast Structural Genomics Consortium Target LbR11.

PDB DOI: https://doi.org/10.2210/pdb3MI6/pdb

Classification: HYDROLASE
Organism(s): Levilactobacillus brevis ATCC 367
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-04-09 Released: 2010-04-28
Deposition Author(s): Vorobiev, S., Chen, Y., Seetharaman, J., Belote, R., Sahdev, S., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.241 (Depositor), 0.236 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3MI6

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

Literature

Crystal structure of the alpha-galactosidase from Lactobacillus brevis.

Vorobiev, S., Chen, Y., Seetharaman, J., Belote, R., Sahdev, S., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 347.04 kDa
Atom Count: 24,417
Modeled Residue Count: 2,958
Deposited Residue Count: 2,980
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-galactosidase	A, B, C, D	745	Levilactobacillus brevis ATCC 367	Mutation(s): 0 Gene Names: LVIS_1758 EC: 3.2.1.22
UniProt
Find proteins for Q03PP7 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947)) Explore Q03PP7 Go to UniProtKB: Q03PP7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03PP7
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: 2.70 Å
R-Value Free: 0.241 (Depositor), 0.236 (DCC)
R-Value Work: 0.173 (Depositor), 0.173 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.938	α = 90
b = 158.818	β = 90
c = 166.017	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXDE	phasing
PHENIX	refinement
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-04-28

Deposition Author(s):

Seetharaman, J.

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-04-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary