3EFB | pdb_00003efb

Crystal Structure of Probable sor Operon Regulator from Shigella flexneri

PDB DOI: https://doi.org/10.2210/pdb3EFB/pdb

Classification: TRANSCRIPTION
Organism(s): Shigella flexneri 2a str. 2457T
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-08 Released: 2008-09-23
Deposition Author(s): Kim, Y., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.249 (Depositor), 0.191 (DCC)
R-Value Work:
0.200 (Depositor), 0.194 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Probable sor Operon Regulator from Shigella flexneri

Kim, Y., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 118.09 kDa
Atom Count: 8,130
Modeled Residue Count: 962
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable sor-operon regulator	A, B, C, D	266	Shigella flexneri 2a str. 2457T	Mutation(s): 0
UniProt
Find proteins for A0A0H2V3A6 (Shigella flexneri) Explore A0A0H2V3A6 Go to UniProtKB: A0A0H2V3A6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2V3A6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.249 (Depositor), 0.191 (DCC)
R-Value Work: 0.200 (Depositor), 0.194 (DCC)
R-Value Observed: 0.203 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.536	α = 90
b = 238.463	β = 90
c = 53.759	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-09-23

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2008-09-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-10-30
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.