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- PDB-1zyn: Oxidized structure of the N-terminal domain of Salmonella typhimu... -

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Basic information

Entry
Database: PDB / ID: 1zyn
TitleOxidized structure of the N-terminal domain of Salmonella typhimurium AhpF
ComponentsAlkyl hydroperoxide reductase subunit F
KeywordsOXIDOREDUCTASE / thiolate
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor / alkyl hydroperoxide reductase activity / thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / response to reactive oxygen species / NAD binding / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
Glutaredoxin - #80 / Alkyl hydroperoxide reductase subunit F / AhpF, N-terminal domain, C-terminal TRX-fold subdomain / AhpF, N-terminal domain, N-terminal TRX-fold subdomain / Thioredoxin domain / : / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / Thioredoxin-like fold / Glutaredoxin domain profile. ...Glutaredoxin - #80 / Alkyl hydroperoxide reductase subunit F / AhpF, N-terminal domain, C-terminal TRX-fold subdomain / AhpF, N-terminal domain, N-terminal TRX-fold subdomain / Thioredoxin domain / : / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / Thioredoxin-like fold / Glutaredoxin domain profile. / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alkyl hydroperoxide reductase subunit F
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRoberts, B.R. / Wood, Z.A. / Jonsson, T.J. / Poole, L.B. / Karplus, P.A.
CitationJournal: Protein Sci. / Year: 2005
Title: Oxidized and synchrotron cleaved structures of the disulfide redox center in the N-terminal domain of Salmonella typhimurium AhpF
Authors: Roberts, B.R. / Wood, Z.A. / Jonsson, T.J. / Poole, L.B. / Karplus, P.A.
History
DepositionJun 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkyl hydroperoxide reductase subunit F
B: Alkyl hydroperoxide reductase subunit F


Theoretical massNumber of molelcules
Total (without water)44,6352
Polymers44,6352
Non-polymers00
Water3,873215
1
A: Alkyl hydroperoxide reductase subunit F


Theoretical massNumber of molelcules
Total (without water)22,3171
Polymers22,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alkyl hydroperoxide reductase subunit F


Theoretical massNumber of molelcules
Total (without water)22,3171
Polymers22,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.603, 108.603, 85.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Alkyl hydroperoxide reductase subunit F / Alkyl hydroperoxide reductase F52A protein


Mass: 22317.385 Da / Num. of mol.: 2 / Fragment: residues 1-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: ahpF / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P19480, Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 30-35% PEG 4000, 0.2M ammonium acetate, 0.1M Tris, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 22423

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2211 -random
Rwork0.199 ---
all-23254 --
obs-22423 96.4 %-
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 0 215 3255

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