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

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Basic information

Entry
Database: PDB / ID: 4ykg
TitleCrystal Structure of the Alkylhydroperoxide Reductase subunit F (AhpF) with NAD+ 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 / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-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: 2.4 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 / struct_conn_type
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_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)59,46621
Polymers56,2751
Non-polymers3,19120
Water2,846158
1
A: Alkyl hydroperoxide reductase subunit F
hetero molecules

A: Alkyl hydroperoxide reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,93142
Polymers112,5502
Non-polymers6,38240
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area15710 Å2
ΔGint-244 kcal/mol
Surface area46780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.882, 59.576, 121.508
Angle α, β, γ (deg.)90.00, 111.40, 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: 56274.871 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, 178 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.2 Å3/Da / Density % sol: 61.57 %
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: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 26052 / % possible obs: 91.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.648 / % possible all: 90.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
DENZOdata collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O5Q

4o5q


Resolution: 2.4→27 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.87 / SU B: 14.976 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.428 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1317 5.1 %RANDOM
Rwork0.221 ---
obs0.224 24472 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20.11 Å2
2---2.48 Å20 Å2
3---2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.4→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3949 0 193 158 4300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194201
X-RAY DIFFRACTIONr_bond_other_d0.0010.024031
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9865695
X-RAY DIFFRACTIONr_angle_other_deg0.78439293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1225522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.46525.119168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49615706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5121521
X-RAY DIFFRACTIONr_chiral_restr0.0850.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02865
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_it2.3864.072085
X-RAY DIFFRACTIONr_mcbond_other2.3864.0692084
X-RAY DIFFRACTIONr_mcangle_it3.8486.0982605
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: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 82 -
Rwork0.26 1774 -
obs--89.75 %
Refinement TLS params.Method: refined / Origin x: 44.14 Å / Origin y: -6.286 Å / Origin z: 84.205 Å
111213212223313233
T0.0933 Å20.0121 Å2-0.0263 Å2-0.01 Å20.0077 Å2--0.102 Å2
L0.0166 °2-0.0125 °2-0.0521 °2-0.096 °20.0666 °2--0.1947 °2
S0.0218 Å °0.0011 Å °0.0111 Å °-0.0636 Å °0.0002 Å °0.0249 Å °-0.0549 Å °-0.0069 Å °-0.0219 Å °

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