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- PDB-4xvg: Crystal structure of Alkylhydroperoxide Reductase Subunit AhpF fr... -

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Basic information

Entry
Database: PDB / ID: 4xvg
TitleCrystal structure of Alkylhydroperoxide Reductase Subunit AhpF from Escherichia coli
ComponentsAlkyl hydroperoxide reductase subunit F
KeywordsOXIDOREDUCTASE / Alkylhydroperoxide Reductase
Function / homology
Function and homology information


alkyl hydroperoxide reductase complex / Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor / alkyl hydroperoxide reductase activity / thioredoxin-disulfide reductase (NADPH) activity / FAD binding / cell redox homeostasis / response to reactive oxygen species / hydrogen peroxide catabolic process / NAD binding / response to oxidative stress / cytosol
Similarity search - Function
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. / Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin-like fold / Glutaredoxin domain profile. ...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. / Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin-like fold / Glutaredoxin domain profile. / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Alkyl hydroperoxide reductase subunit F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, C.F. / Gao, Z.Q. / Dong, Y.H. / Liu, Q.S.
CitationJournal: To Be Published
Title: Crystal structure of Alkylhydroperoxide Reductase Subunit AhpF from Escherichia coli
Authors: Chen, C.F. / Gao, Z.Q. / Dong, Y.H. / Liu, Q.S.
History
DepositionJan 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkyl hydroperoxide reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0282
Polymers56,2431
Non-polymers7861
Water4,504250
1
A: Alkyl hydroperoxide reductase subunit F
hetero molecules

A: Alkyl hydroperoxide reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0574
Polymers112,4862
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7550 Å2
ΔGint-34 kcal/mol
Surface area43330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.040, 58.625, 94.941
Angle α, β, γ (deg.)90.00, 103.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 56242.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ahpF, b0606, JW0599 / Production host: Escherichia coli (E. coli)
References: UniProt: P35340, Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Ammonium citrate tribasic, pH 7.0 20 % w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 28666 / Num. obs: 28666 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 20.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 4.69 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1HYU

1hyu


Resolution: 2.2→46.155 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 1467 5.12 %random
Rwork0.1779 ---
obs0.1804 28657 97.29 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.643 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.0813 Å20 Å2-2.5115 Å2
2---5.5598 Å2-0 Å2
3---10.641 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 53 250 4222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084049
X-RAY DIFFRACTIONf_angle_d1.0355494
X-RAY DIFFRACTIONf_dihedral_angle_d15.8141490
X-RAY DIFFRACTIONf_chiral_restr0.069634
X-RAY DIFFRACTIONf_plane_restr0.005710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27420.31351300.21582639X-RAY DIFFRACTION95
2.2742-2.36520.26451450.19552698X-RAY DIFFRACTION97
2.3652-2.47290.25261340.19512686X-RAY DIFFRACTION97
2.4729-2.60320.28021470.18912678X-RAY DIFFRACTION97
2.6032-2.76630.25791590.19572655X-RAY DIFFRACTION96
2.7663-2.97990.27231370.19522675X-RAY DIFFRACTION96
2.9799-3.27970.22041480.18952750X-RAY DIFFRACTION98
3.2797-3.75410.21371630.16942762X-RAY DIFFRACTION99
3.7541-4.7290.17461540.14382787X-RAY DIFFRACTION99
4.729-46.16540.20171500.17442860X-RAY DIFFRACTION99

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