3DCD | pdb_00003dcd

X-ray structure of the galactose mutarotase related enzyme Q5FKD7 from Lactobacillus acidophilus at the resolution 1.9A. Northeast Structural Genomics consortium target LaR33.

PDB DOI: https://doi.org/10.2210/pdb3DCD/pdb

Classification: structural genomics, unknown function
Organism(s): Lactobacillus acidophilus
Mutation(s): No

Deposited: 2008-06-03 Released: 2008-07-29
Deposition Author(s): Kuzin, A.P., Lew, S., Vorobiev, S.M., Seetharaman, J., Wang, H., Mao, L., Foote, E.L., Xiao, R., Nair, R., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.206 (Depositor), 0.205 (DCC)
R-Value Work:
0.178 (Depositor), 0.177 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

X-ray structure of the galactose mutarotase related enzyme Q5FKD7 from Lactobacillus acidophilus at the resolution 1.9A. Northeast Structural Genomics consortium target LaR33. (CASP Target)

Kuzin, A.P., Lew, S., Vorobiev, S.M., Seetharaman, J., Wang, H., Mao, L., Foote, E.L., Xiao, R., Nair, R., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 72.35 kDa
Atom Count: 5,420
Modeled Residue Count: 600
Deposited Residue Count: 614
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose mutarotase related enzyme	A, B	307	Lactobacillus acidophilus	Mutation(s): 0
UniProt
Find proteins for Q5FKD7 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)) Explore Q5FKD7 Go to UniProtKB: Q5FKD7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5FKD7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.206 (Depositor), 0.205 (DCC)
R-Value Work: 0.178 (Depositor), 0.177 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.27	α = 90
b = 88.27	β = 90
c = 139.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-07-29

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-07-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Advisory, Refinement description
Version 1.3: 2024-10-30
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary