4EJO | pdb_00004ejo

Crystal structure of padr family transcriptional regulator from Eggerthella lenta DSM 2243

PDB DOI: https://doi.org/10.2210/pdb4EJO/pdb
Entry: 4EJO supersedes: 3RI2

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

Deposited: 2012-04-06 Released: 2012-04-25
Deposition Author(s): Chang, C., Li, H., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.235 (Depositor), 0.209 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4EJO

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

Literature

Crystal structure of padr family transcriptional regulator from Eggerthella lenta DSM 2243

Chang, C., Li, H., Bearden, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 28.27 kDa
Atom Count: 1,852
Modeled Residue Count: 224
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, PadR-like family	A, B	123	Eggerthella lenta DSM 2243	Mutation(s): 0 Gene Names: Elen_1533
UniProt
Find proteins for C8WHB0 (Eggerthella lenta (strain ATCC 25559 / DSM 2243 / CCUG 17323 / JCM 9979 / KCTC 3265 / NCTC 11813 / VPI 0255 / 1899 B)) Explore C8WHB0 Go to UniProtKB: C8WHB0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C8WHB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EOH Query on EOH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	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: 0.235 (Depositor), 0.209 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Diffraction Data:

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.783	α = 90
b = 55.783	β = 90
c = 132.425	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-04-25

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 3RI2

Revision History (Full details and data files)

Version 1.0: 2012-04-25
Type: Initial release
Version 1.1: 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.