3GEK | pdb_00003gek

Crystal structure of putative thioesterase yhdA from Lactococcus lactis. Northeast Structural Genomics Consortium Target KR113

PDB DOI: https://doi.org/10.2210/pdb3GEK/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Lactococcus lactis subsp. lactis Il1403
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-02-25 Released: 2009-03-17
Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, R., Lee, D., Foote, E.L., Ciccosanti, C., Janjua, H., Xiao, R., Nair, R., Rost, B., 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: 2.24 Å
R-Value Free:
0.255 (Depositor), 0.266 (DCC)
R-Value Work:
0.224 (Depositor), 0.252 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

X-Ray structure of putative thioesterase yhdA from Lactococcus lactis. Northeast Structural Genomics Consortium Target KR113

Kuzin, A.P., Su, M., Seetharaman, R., Lee, D., Foote, E.L., Ciccosanti, C., Janjua, H., Xiao, R., Nair, R., Rost, B., Acton, T.B., Everett, J.K., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 65.94 kDa
Atom Count: 3,986
Modeled Residue Count: 507
Deposited Residue Count: 584
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative thioesterase yhdA	A, B, C, D	146	Lactococcus lactis subsp. lactis Il1403	Mutation(s): 7 Gene Names: L131, L131392, LL0726, yhdA
UniProt
Find proteins for Q9CHK5 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CHK5 Go to UniProtKB: Q9CHK5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CHK5
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: 2.24 Å
R-Value Free: 0.255 (Depositor), 0.266 (DCC)
R-Value Work: 0.224 (Depositor), 0.252 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.948	α = 90
b = 64.056	β = 90
c = 144.657	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-09-06
Changes: Data collection, Refinement description
Version 1.4: 2023-11-22
Changes: Data collection
Version 1.5: 2024-10-16
Changes: Structure summary