4PZJ

1.60 Angstrom resolution crystal structure of a transcriptional regulator of the LysR family from Eggerthella lenta DSM 2243

PDB DOI: https://doi.org/10.2210/pdb4PZJ/pdb

Classification: TRANSCRIPTION
Organism(s): Eggerthella lenta DSM 2243
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-03-31 Released: 2014-04-23
Deposition Author(s): Halavaty, A.S., Filippova, E.V., Minasov, G., Kiryukhina, O., Endres, M., Shuvalova, L., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.213
R-Value Work: 0.190
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

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

Literature

1.60 Angstrom resolution crystal structure of a transcriptional regulator of the LysR family from Eggerthella lenta DSM 2243

Halavaty, A.S., Filippova, E.V., Minasov, G., Kiryukhina, O., Endres, M., Shuvalova, L., Joachimiak, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 8.21 kDa
Atom Count: 651
Modelled Residue Count: 70
Deposited Residue Count: 70
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LysR family	A	70	Eggerthella lenta DSM 2243	Mutation(s): 0 Gene Names: Elen_0221
UniProt
Find proteins for C8WJY2 (Eggerthella lenta (strain ATCC 25559 / DSM 2243 / CCUG 17323 / JCM 9979 / KCTC 3265 / NCTC 11813 / VPI 0255 / 1899 B)) Explore C8WJY2 Go to UniProtKB: C8WJY2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C8WJY2
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 B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.213
R-Value Work: 0.190
R-Value Observed: 0.191
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.623	α = 90
b = 31.623	β = 90
c = 132.34	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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-04-23

Deposition Author(s):

Filippova, E.V.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-04-23
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.