5IM2 | pdb_00005im2

Crystal structure of a TRAP solute binding protein from Rhodoferax ferrireducens T118 (Rfer_2570, TARGET EFI-510210) in complex with copurified benzoate

PDB DOI: https://doi.org/10.2210/pdb5IM2/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Rhodoferax ferrireducens T118
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-03-05 Released: 2016-03-23
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.199 (Depositor), 0.200 (DCC)
R-Value Work:
0.157 (Depositor), 0.159 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a TRAP solute binding protein from Rhodoferax ferrireducens T118 (Rfer_2570, TARGET EFI-510210) in complex with copurified benzoate

Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 42.26 kDa
Atom Count: 2,754
Modeled Residue Count: 322
Deposited Residue Count: 385
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Twin-arginine translocation pathway signal	A	385	Rhodoferax ferrireducens T118	Mutation(s): 0 Gene Names: Rfer_2570
UniProt
Find proteins for Q21VB6 (Albidiferax ferrireducens (strain ATCC BAA-621 / DSM 15236 / T118)) Explore Q21VB6 Go to UniProtKB: Q21VB6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q21VB6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEZ Query on BEZ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.199 (Depositor), 0.200 (DCC)
R-Value Work: 0.157 (Depositor), 0.159 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.014	α = 90
b = 71.864	β = 90
c = 78.603	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
MOSFLM	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-03-23

Deposition Author(s):

Al Obaidi, N.F.

Wasserman, S.R.

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2016-03-23
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, 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.