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- PDB-1fl2: CATALYTIC CORE COMPONENT OF THE ALKYLHYDROPEROXIDE REDUCTASE AHPF... -

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Basic information

Entry
Database: PDB / ID: 1fl2
TitleCATALYTIC CORE COMPONENT OF THE ALKYLHYDROPEROXIDE REDUCTASE AHPF FROM E.COLI
ComponentsALKYL HYDROPEROXIDE REDUCTASE SUBUNIT F
KeywordsOXIDOREDUCTASE / alkylhydroperoxide reductase / reactive oxygen / FAD / disulphide oxidoreductase
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 / response to reactive oxygen species / cell redox homeostasis / 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. / FAD/NAD(P)-binding domain ...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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Alkyl hydroperoxide reductase subunit F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsBieger, B. / Essen, L.-O.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the catalytic core component of the alkylhydroperoxide reductase AhpF from Escherichia coli.
Authors: Bieger, B. / Essen, L.O.
History
DepositionAug 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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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)34,1977
Polymers32,9321
Non-polymers1,2666
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: ALKYL HYDROPEROXIDE REDUCTASE SUBUNIT F
hetero molecules

A: ALKYL HYDROPEROXIDE REDUCTASE SUBUNIT F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,39514
Polymers65,8632
Non-polymers2,53212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area9000 Å2
ΔGint-148 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.440, 60.440, 171.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-840-

HOH

21A-877-

HOH

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Components

#1: Protein ALKYL HYDROPEROXIDE REDUCTASE SUBUNIT F / ALKYL HYDROPEROXIDE REDUCTASE F52A PROTEIN


Mass: 32931.531 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0 M ammonium sulfate, 6% PEG 400, 0.1 M Tris/acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Temperature: 291 K / pH: 8 / Details: Bieger, B., (2000) Acta Crystallogr. D56, 92.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
25 mMTris-HCl1drop
32.0 Mammonium sulfate1reservoir
46 %PEG4001reservoir
50.1 MTris-acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 29657 / Num. obs: 126257 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.109 / % possible all: 99.2
Reflection
*PLUS
Num. obs: 29657 / Num. measured all: 126257
Reflection shell
*PLUS
% possible obs: 99.2 % / Mean I/σ(I) obs: 12.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 1.9→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2267834.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1447 4.9 %RANDOM
Rwork0.197 ---
all0.197 126257 --
obs0.197 29484 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.86 Å2 / ksol: 0.418 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0.31 Å20 Å2
2--0.21 Å20 Å2
3----0.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 78 409 2798
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.53
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.225 232 4.8 %
Rwork0.199 4573 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FAD.PARAMFAD.TOP
X-RAY DIFFRACTION3PARAM.PO4TOP.PO4
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.53

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