3DQP | pdb_00003dqp

Crystal structure of the oxidoreductase ylbE from Lactococcus lactis, Northeast Structural Genomics Consortium Target KR121.

PDB DOI: https://doi.org/10.2210/pdb3DQP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lactococcus lactis subsp. lactis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-07-09 Released: 2008-09-09
Deposition Author(s): Forouhar, F., Neely, H., Seetharaman, J., Mao, L., Xiao, R., Ciccosanti, C., Foote, E.L., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.167 (Depositor), 0.172 (DCC)
R-Value Work:
0.165 (Depositor), 0.172 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the oxidoreductase ylbE from Lactococcus lactis, Northeast Structural Genomics Consortium Target KR121.

Forouhar, F., Neely, H., Seetharaman, J., Mao, L., Xiao, R., Ciccosanti, C., Foote, E.L., Lee, D., Everett, J.K., B Acton, T., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 24.52 kDa
Atom Count: 2,169
Modeled Residue Count: 219
Deposited Residue Count: 219
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase ylbE	A	219	Lactococcus lactis subsp. lactis	Mutation(s): 1 Gene Names: ylbE, LL1109, L119, L119013
UniProt
Find proteins for Q9CGI7 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CGI7 Go to UniProtKB: Q9CGI7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CGI7
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.167 (Depositor), 0.172 (DCC)
R-Value Work: 0.165 (Depositor), 0.172 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.567	α = 90
b = 34.79	β = 102.91
c = 66.379	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

Seetharaman, J.

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2024-10-09
Changes: Data collection, Structure summary

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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.