3LQ1 | pdb_00003lq1

Crystal structure of 2-succinyl-6-hydroxy-2,4-cyclohexadiene 1-carboxylic acid synthase/2-oxoglutarate decarboxylase FROM Listeria monocytogenes str. 4b F2365

PDB DOI: https://doi.org/10.2210/pdb3LQ1/pdb

Classification: TRANSFERASE
Organism(s): Listeria monocytogenes serotype 4b str. F2365
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-08 Released: 2010-03-31
Deposition Author(s): Patskovsky, Y., Toro, R., Freeman, J., Hu, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York Structural GenomiX Research Consortium (NYSGXRC), New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.265 (Depositor), 0.267 (DCC)
R-Value Work:
0.222 (Depositor), 0.222 (DCC)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LQ1

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

Literature

Crystal Structure of Sephchc Synthase from Listeria Monocytogenes

Patskovsky, Y., Toro, R., Freeman, J., Hu, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 129.09 kDa
Atom Count: 8,131
Modeled Residue Count: 1,031
Deposited Residue Count: 1,156
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase	A, B	578	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0 Gene Names: menD, LMOf2365_1699, PRK07449 EC: 2.2.1.9
UniProt
Find proteins for Q71YZ2 (Listeria monocytogenes serotype 4b (strain F2365)) Explore Q71YZ2 Go to UniProtKB: Q71YZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q71YZ2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.265 (Depositor), 0.267 (DCC)
R-Value Work: 0.222 (Depositor), 0.222 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.695	α = 90
b = 99.695	β = 90
c = 259.982	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-31

Deposition Author(s):

New York Structural GenomiX Research Consortium (NYSGXRC)

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-03-31
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: 2018-11-21
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Structure summary
Version 1.5: 2024-02-21
Changes: Data collection, Database references

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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.