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- PDB-4o5u: Crystal structure of Alkylhydroperoxide Reductase subunit F from ... -

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Basic information

Entry
Database: PDB / ID: 4o5u
TitleCrystal structure of Alkylhydroperoxide Reductase subunit F from E. coli at 2.65 Ang resolution
ComponentsAlkyl hydroperoxide reductase subunit F
KeywordsOXIDOREDUCTASE
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
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. / Pyridine nucleotide-disulphide oxidoreductase / 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. / 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 / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / 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 / MAD / Resolution: 2.65 Å
AuthorsKamariah, N. / Dip, P.V. / Manimekalai, M.S.S. / Gruber, G. / Eisenhaber, F. / Eisenhaber, B.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli
Authors: Dip, P.V. / Kamariah, N. / Subramanian Manimekalai, M.S. / Nartey, W. / Balakrishna, A.M. / Eisenhaber, F. / Eisenhaber, B. / Gruber, G.
#1: Journal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of the catalytic core component of the alkylhydroperoxide reductase AhpF from Escherichia coli
Authors: Bieger, B. / Essen, L.O.
#2: Journal: Biochemistry / Year: 2001
Title: Structure of intact AhpF reveals a mirrored thioredoxin-like active site and implies large domain rotations during catalysis
Authors: Wood, Z.A. / Poole, L.B. / Karplus, P.A.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkyl hydroperoxide reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,90911
Polymers56,2431
Non-polymers1,66610
Water2,918162
1
A: Alkyl hydroperoxide reductase subunit F
hetero molecules

A: Alkyl hydroperoxide reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,81922
Polymers112,4862
Non-polymers3,33320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10730 Å2
ΔGint-248 kcal/mol
Surface area45740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.698, 59.598, 123.715
Angle α, β, γ (deg.)90.00, 113.68, 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 natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12
References: UniProt: P35340, Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 296 K / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 2 M ammonium sulfate, 10 mM cadmium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.0, 1.55072, 1.58994, 1.59048
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2011 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.550721
31.589941
41.590481
ReflectionRedundancy: 5.2 % / Number: 46306 / Rmerge(I) obs: 0.169 / Χ2: 0.9 / D res high: 3.45 Å / D res low: 50 Å / Num. obs: 8850 / % possible obs: 92.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.435098.810.0931.1416.5
5.97.4399.510.1431.1036.5
5.155.999.310.1870.9046.4
4.685.1597.410.1830.9025.8
4.354.6895.410.1930.9235.2
4.094.3594.710.2270.8264.9
3.894.099110.3110.7524.7
3.723.8988.810.3520.7084.3
3.573.7283.110.4190.6193.8
3.453.5775.710.4460.5363.3
ReflectionResolution: 2.65→30 Å / Num. obs: 21022 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.9
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.2 / % possible all: 92.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SOLOMONphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
DENZOdata reduction
autoSHARPphasing
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MAD / Resolution: 2.65→28.82 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.857 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 21.11 / Stereochemistry target values: ML
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.22 1055 5.1 %
Rwork0.172 --
obs0.174 20674 98.5 %
all-19647 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å2-0.09 Å2
2--0 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.65→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 94 162 4203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064102
X-RAY DIFFRACTIONf_angle_d0.9085562
X-RAY DIFFRACTIONf_dihedral_angle_d15.8931504
X-RAY DIFFRACTIONf_chiral_restr0.048637
X-RAY DIFFRACTIONf_plane_restr0.004710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6472-2.76760.29121230.23962220X-RAY DIFFRACTION90
2.7676-2.91340.25681320.21412455X-RAY DIFFRACTION99
2.9134-3.09580.27871530.20312433X-RAY DIFFRACTION100
3.0958-3.33450.21781400.17282492X-RAY DIFFRACTION100
3.3345-3.66940.20121140.16692463X-RAY DIFFRACTION100
3.6694-4.1990.20371070.15282510X-RAY DIFFRACTION100
4.199-5.2850.17111370.14132502X-RAY DIFFRACTION100
5.285-28.82050.23591490.17392544X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01530.0102-0.01160.00470.01230.0869-0.3513-0.1080.00670.0836-0.1376-0.19610.1160.1460.00010.65110.07740.05150.73290.15620.372233.887765.2618-15.7287
20.469-0.0632-0.36430.00740.11340.6944-0.0212-0.0576-0.07540.15160.04690.13890.1218-0.16210.00010.5439-0.02640.06980.47360.01310.236319.996269.4531-9.5601
30.00740.01310.00760.0211-0.0020.01580.0183-0.1567-0.09240.4061-0.03610.3329-0.139-0.002700.8051-0.01520.14540.6616-0.0990.412714.503184.3159-2.1695
40.1411-0.06520.01940.2392-0.14850.11340.0588-0.1539-0.230.16880.04990.6057-0.093-0.08530.00351.1426-0.06330.16420.73620.03430.391516.469468.641115.7927
50.39010.23360.16530.6555-0.14730.1389-0.00480.25060.3646-0.04170.0934-0.0397-0.0657-0.15160.05150.12170.0038-0.04180.10940.0620.205624.198362.615845.0913
60.2076-0.0446-0.13530.28420.01950.3197-0.01360.3550.0951-0.2338-0.02030.2523-0.07050.0186-0.00630.1611-0.0157-0.02570.22680.00950.096421.756750.709734.4207
70.46950.0107-0.06361.0581-0.12950.6636-0.0383-0.04280.01870.0527-0.0638-0.06140.0203-0.0688-0.00140.1216-0.00610.00970.1404-0.0110.21651.525954.935466.8438
80.3153-0.0040.070.13480.13660.3539-0.0935-0.0387-0.11910.01480.03790.00940.02110.0543-0.10940.0785-0.0019-0.01680.0594-0.00530.155318.715348.539651.5162
90.0114-0.0071-0.01050.00290.00640.00570.0927-0.0438-0.1606-0.03290.0975-0.0562-0.0997-0.02660.00020.186-0.0670.0570.3902-0.040.356740.430144.475836.2343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 186 )
4X-RAY DIFFRACTION4chain 'A' and (resid 187 through 206 )
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 280 )
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 325 )
7X-RAY DIFFRACTION7chain 'A' and (resid 326 through 437 )
8X-RAY DIFFRACTION8chain 'A' and (resid 438 through 514 )
9X-RAY DIFFRACTION9chain 'A' and (resid 515 through 521 )

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