3E19 | pdb_00003e19

Crystal Structure of Iron Uptake Regulatory Protein (FeoA) Solved by Sulfur SAD in a Monoclinic Space Group

PDB DOI: https://doi.org/10.2210/pdb3E19/pdb

Classification: TRANSCRIPTION REGULATOR, METAL BINDING PROTEIN
Organism(s): Thermococcus thioreducens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-02 Released: 2008-12-16
Deposition Author(s): Hughes, R.C., Li, Y., Wang, B.-C., Liu, Z.-J., Ng, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.228 (Depositor), 0.233 (DCC)
R-Value Work:
0.173 (Depositor), 0.181 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Crystallographic Structure Determination of Iron Uptake Regulatory Protein (FeoA) by Sulfur SAD in a Monoclinic Space Group

Hughes, R.C., Li, Y., Wang, B.-C., Liu, Z.-J., Ng, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 32.12 kDa
Atom Count: 2,346
Modeled Residue Count: 299
Deposited Residue Count: 308
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FeoA	A, B, C, D	77	Thermococcus thioreducens	Mutation(s): 0 Gene Names: OGL-20_FeoA
UniProt
Find proteins for D0VWU5 (Thermococcus thioreducens) Explore D0VWU5 Go to UniProtKB: D0VWU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.228 (Depositor), 0.233 (DCC)
R-Value Work: 0.173 (Depositor), 0.181 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.786	α = 90
b = 68.386	β = 132.67
c = 68.969	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-12-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description

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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.