4K15

2.75 Angstrom Crystal Structure of Hypothetical Protein lmo2686 from Listeria monocytogenes EGD-e

PDB DOI: https://doi.org/10.2210/pdb4K15/pdb

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

Deposited: 2013-04-04 Released: 2013-04-17
Deposition Author(s): Minasov, G., Wawrzak, Z., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.240
R-Value Work: 0.196
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

2.75 Angstrom Crystal Structure of Hypothetical Protein lmo2686 from Listeria monocytogenes EGD-e

Minasov, G., Wawrzak, Z., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 58.78 kDa
Atom Count: 3,195
Modelled Residue Count: 398
Deposited Residue Count: 525
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo2686 protein	A, B, C	175	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: lmo2686
UniProt
Find proteins for Q8Y3Z3 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y3Z3 Go to UniProtKB: Q8Y3Z3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8Y3Z3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth C]	D [auth A], E [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [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: 2.75 Å
R-Value Free: 0.240
R-Value Work: 0.196
R-Value Observed: 0.198
Space Group: P 3₂ 2 1
Diffraction Data: https://doi.org/10.18430/M34K15

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.093	α = 90
b = 91.093	β = 90
c = 125.47	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-04-17

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2013-04-17
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description

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 R01GM133198.