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- PDB-4ykf: Crystal Structure of the Alkylhydroperoxide Reductase subunit F (... -

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Basic information

Entry
Database: PDB / ID: 4ykf
TitleCrystal Structure of the Alkylhydroperoxide Reductase subunit F (AhpF) with NADH from Escherichia coli
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 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Alkyl hydroperoxide reductase subunit F
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsKamariah, N. / Manimekalai, M.S.S. / Gruber, G. / Eisenhaber, F. / Eisenhaber, B.
Citation
Journal: Biochim.Biophys.Acta / Year: 2015
Title: Crystallographic and solution studies of NAD(+)- and NADH-bound alkylhydroperoxide reductase subunit F (AhpF) from Escherichia coli provide insight into sequential enzymatic steps
Authors: Kamariah, N. / Manimekalai, M.S.S. / Nartey, W. / Eisenhaber, F. / Eisenhaber, B. / Gruber, G.
#1: 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. / Manimekalai, M.S.S. / Nartey, W. / Balakrishna, A.M. / Eisenhaber, F. / Eisenhaber, B. / Gruber, G.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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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)59,36220
Polymers56,2431
Non-polymers3,11919
Water2,558142
1
A: Alkyl hydroperoxide reductase subunit F
hetero molecules

A: Alkyl hydroperoxide reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,72340
Polymers112,4862
Non-polymers6,23738
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area15100 Å2
ΔGint-266 kcal/mol
Surface area46500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.090, 59.390, 121.350
Angle α, β, γ (deg.)90.00, 111.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-716-

HOH

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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 genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 / Gene: ahpF, b0606, JW0599 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Gami 2
References: UniProt: P35340, Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 7 types, 161 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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 61.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Na-Hepes, 2.5 % (v/v) PEG 400, 2 M ammonium sulfate, 10 mM cadmium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2014 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.5→49.87 Å / Num. obs: 22917 / % possible obs: 92.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.5 / % possible all: 85.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
DENZOdata collection
SCALA0.1.26data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O5Q

4o5q


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.833 / SU B: 16.838 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.571 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1168 5.1 %RANDOM
Rwork0.225 ---
obs0.228 21672 91.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20.37 Å2
2---2.93 Å20 Å2
3---2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 187 142 4276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194189
X-RAY DIFFRACTIONr_bond_other_d0.0010.024022
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9845680
X-RAY DIFFRACTIONr_angle_other_deg0.8183.0019268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2475520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56525.119168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.715707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7411521
X-RAY DIFFRACTIONr_chiral_restr0.0860.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02863
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0843.0922083
X-RAY DIFFRACTIONr_mcbond_other2.0813.0912082
X-RAY DIFFRACTIONr_mcangle_it3.3454.6322602
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 60 -
Rwork0.276 1463 -
obs--84.42 %
Refinement TLS params.Method: refined / Origin x: -25.5586 Å / Origin y: 59.3634 Å / Origin z: 142.0154 Å
111213212223313233
T0.0565 Å2-0.0012 Å2-0.0423 Å2-0.0735 Å20.0019 Å2--0.1027 Å2
L0.0039 °2-0.0122 °2-0.0109 °2-0.0851 °20.0299 °2--0.3041 °2
S0.0113 Å °-0.0126 Å °-0.0075 Å °-0.0675 Å °0.0194 Å °0.0522 Å °-0.0437 Å °-0.0245 Å °-0.0307 Å °

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