4XVG | pdb_00004xvg

Crystal structure of Alkylhydroperoxide Reductase Subunit AhpF from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb4XVG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-01-27 Released: 2016-02-24
Deposition Author(s): Chen, C.F., Gao, Z.Q., Dong, Y.H., Liu, Q.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.225 (Depositor), 0.220 (DCC)
R-Value Work:
0.178 (Depositor), 0.176 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of Alkylhydroperoxide Reductase Subunit AhpF from Escherichia coli

Chen, C.F., Gao, Z.Q., Dong, Y.H., Liu, Q.S.

To be published.

Macromolecule Content

Total Structure Weight: 57.03 kDa
Atom Count: 4,231
Modeled Residue Count: 519
Deposited Residue Count: 521
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkyl hydroperoxide reductase subunit F	A	521	Escherichia coli K-12	Mutation(s): 0 Gene Names: ahpF, b0606, JW0599 EC: 1.8.1
UniProt
Find proteins for P35340 (Escherichia coli (strain K12)) Explore P35340 Go to UniProtKB: P35340
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35340
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD 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]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.225 (Depositor), 0.220 (DCC)
R-Value Work: 0.178 (Depositor), 0.176 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.04	α = 90
b = 58.625	β = 103.52
c = 94.941	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-02-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-02-24
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: 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.