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- PDB-4o5q: Crystal Structure of the Alkylhydroperoxide Reductase AhpF from E... -

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Basic information

Entry
Database: PDB / ID: 4o5q
TitleCrystal Structure of the Alkylhydroperoxide Reductase AhpF from Escherichia coli
ComponentsAlkyl hydroperoxide reductase subunit F
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


alkyl hydroperoxide reductase complex / alkyl hydroperoxide reductase activity / Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor / NADH-dependent peroxiredoxin activity / thioredoxin-disulfide reductase (NADPH) activity / FAD binding / cell redox homeostasis / response to reactive oxygen species / hydrogen peroxide catabolic process / NAD binding ...alkyl hydroperoxide reductase complex / alkyl hydroperoxide reductase activity / Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor / NADH-dependent peroxiredoxin 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 - #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 / FAD/NAD(P)-binding domain superfamily / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / Alkyl hydroperoxide reductase subunit F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDip, P.V. / Kamariah, N. / Manimekalai, M.S.S. / Balakrishna, A.M. / Gruber, G.
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
Revision 1.3Nov 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_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)59,77126
Polymers56,2431
Non-polymers3,52925
Water9,062503
1
A: Alkyl hydroperoxide reductase subunit F
hetero molecules

A: Alkyl hydroperoxide reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,54352
Polymers112,4862
Non-polymers7,05750
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area22960 Å2
ΔGint-212 kcal/mol
Surface area44470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.494, 58.696, 123.994
Angle α, β, γ (deg.)90.00, 114.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 8 types, 528 molecules

#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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 0.1M Na-Hepes, 2.5%(v/v) PEG400, 2M ammonium sulfate, 10mM cadmium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7.3 % / Number: 346921 / Rmerge(I) obs: 0.067 / Χ2: 0.53 / D res high: 2 Å / D res low: 30 Å / Num. obs: 47455 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.313099.510.0320.6817.3
3.424.3199.610.0510.6867.4
2.993.4299.910.0550.7077.5
2.712.9999.910.0840.5947.5
2.522.7199.910.120.517.5
2.372.5210010.1660.4587.5
2.252.3710010.2130.4387.5
2.152.2510010.2770.4047.4
2.072.1599.910.4040.3817.2
22.0798.610.4960.3646.3
ReflectionResolution: 2→30 Å / Num. obs: 47454 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.1 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
DENZOdata reduction
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HYU

1hyu


Resolution: 2→26.62 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.19 / Isotropic thermal model: Isotropic / σ(F): 1.38 / Phase error: 17.09 / Stereochemistry target values: ML
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.188 2399 5.06 %
Rwork0.141 --
obs0.144 47447 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0.2 Å2
2---0.15 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2→26.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 0 212 503 4663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124294
X-RAY DIFFRACTIONf_angle_d1.4085800
X-RAY DIFFRACTIONf_dihedral_angle_d16.3811616
X-RAY DIFFRACTIONf_chiral_restr0.08649
X-RAY DIFFRACTIONf_plane_restr0.007732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03570.25121240.20292542X-RAY DIFFRACTION95
2.0357-2.07990.22091480.18022618X-RAY DIFFRACTION99
2.0799-2.12830.23141310.16662621X-RAY DIFFRACTION100
2.1283-2.18150.20381510.15162654X-RAY DIFFRACTION100
2.1815-2.24050.18391500.13862660X-RAY DIFFRACTION100
2.2405-2.30630.20541320.13742626X-RAY DIFFRACTION100
2.3063-2.38070.18321280.13242650X-RAY DIFFRACTION100
2.3807-2.46580.18821520.13452644X-RAY DIFFRACTION100
2.4658-2.56440.18351550.12862651X-RAY DIFFRACTION100
2.5644-2.6810.17441210.12482649X-RAY DIFFRACTION100
2.681-2.82220.18481280.1192668X-RAY DIFFRACTION100
2.8222-2.99880.19041500.12732648X-RAY DIFFRACTION100
2.9988-3.230.18751620.132662X-RAY DIFFRACTION100
3.23-3.55440.15061470.12872663X-RAY DIFFRACTION100
3.5544-4.06710.17441270.12632674X-RAY DIFFRACTION100
4.0671-5.11820.16761550.12922660X-RAY DIFFRACTION99
5.1182-26.62290.23331380.18952758X-RAY DIFFRACTION100
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)
10.4943-0.4781-0.08090.479-0.06060.734-0.10270.144-0.05950.20360.06010.01690.1430.0035-0.00050.4717-0.04120.06490.2803-0.00150.1996-30.7928-21.5944-10.5886
2-0.183-0.09050.02980.0583-0.22630.33810.03390.02130.0222-0.13850.0158-0.0223-0.1226-0.07390.01340.28670.0028-0.00940.2380.03610.1945-33.3459-22.420827.5841
30.25110.0584-0.24280.23340.01350.3281-0.0330.02280.02160.03020.01230.13960.0639-0.0188-00.14540.0069-0.02040.1974-0.01760.2457-49.9456-34.72261.9526
40.1740.13890.08770.4532-0.12370.147-0.03710.0121-0.0137-0.07040.0291-0.01810.015-0.012700.1369-0.0119-0.00420.16430.00060.1781-29.5825-42.777546.8206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 150 )
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 300 )
3X-RAY DIFFRACTION3chain 'A' and (resid 301 through 450 )
4X-RAY DIFFRACTION4chain 'A' and (resid 451 through 521 )

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