4GQO | pdb_00004gqo

2.1 Angstrom resolution crystal structure of uncharacterized protein lmo0859 from Listeria monocytogenes EGD-e

PDB DOI: https://doi.org/10.2210/pdb4GQO/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-23 Released: 2012-09-19
Deposition Author(s): Halavaty, A.S., Filippova, E.V., Minasov, G., Dubrovska, I., Winsor, J., Shuvalova, L., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.211 (Depositor), 0.211 (DCC)
R-Value Work:
0.165 (Depositor), 0.167 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

2.1 Angstrom resolution crystal structure of uncharacterized protein lmo0859 from Listeria monocytogenes EGD-e

Halavaty, A.S., Filippova, E.V., Minasov, G., Dubrovska, I., Winsor, J., Shuvalova, L., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 148.65 kDa
Atom Count: 10,613
Modeled Residue Count: 1,212
Deposited Residue Count: 1,299
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo0859 protein	A, B, C	433	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: lmo0859
UniProt
Find proteins for Q8Y8N7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y8N7 Go to UniProtKB: Q8Y8N7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Y8N7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.211 (Depositor), 0.211 (DCC)
R-Value Work: 0.165 (Depositor), 0.167 (DCC)
R-Value Observed: 0.167 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.865	α = 90
b = 120.033	β = 90
c = 221.448	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-09-19

Deposition Author(s):

Filippova, E.V.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-09-19
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, 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.