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- PDB-5h29: Crystal Structure of the NTD_N/C domain of Alkylhydroperoxide Red... -

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Basic information

Entry
Database: PDB / ID: 5h29
TitleCrystal Structure of the NTD_N/C domain of Alkylhydroperoxide Reductase AhpF from Enterococcus Faecalis (V583)
ComponentsThioredoxin reductase/glutathione-related protein
KeywordsOXIDOREDUCTASE / Electron donor / Thioredoxin fold / FAD Binding
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Alkyl hydroperoxide reductase F subunit homogue, putative / AhpF, N-terminal domain, C-terminal TRX-fold subdomain / AhpF, N-terminal domain, N-terminal TRX-fold subdomain / Thioredoxin domain / : / Thioredoxin-like fold / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
PROLINE / Thioredoxin reductase/glutathione-related protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBalakrishna, A.M. / Kwang, T.Y. / Gruber, G.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Novel insights into the vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F
Authors: Toh, Y.K. / Balakrishna, A.M. / Manimekalai, M.S.S. / Chionh, B.B. / Seetharaman, R.R.C. / Eisenhaber, F. / Eisenhaber, B. / Gruber, G.
History
DepositionOct 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 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: Thioredoxin reductase/glutathione-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6204
Polymers24,2861
Non-polymers3333
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.278, 134.278, 134.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Thioredoxin reductase/glutathione-related protein


Mass: 24286.342 Da / Num. of mol.: 1 / Fragment: UNP residues 354-560
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: EF_2738 / Plasmid: pET9D / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q830N9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
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: 4.15 Å3/Da / Density % sol: 71.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris (pH 6.5), 2.0 M ammonium sulfate and 0.1 M sodium 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: Oct 15, 2015 / Details: mirrors
RadiationMonochromator: Double Crystal Si(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 19025 / % possible obs: 99.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 56.58 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / CC1/2: 0.88 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZYN

1zyn


Resolution: 2.3→29.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.385 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.167 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22871 931 4.9 %RANDOM
Rwork0.19386 ---
obs0.19558 18028 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.827 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 21 106 1730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191672
X-RAY DIFFRACTIONr_bond_other_d0.0010.021670
X-RAY DIFFRACTIONr_angle_refined_deg0.9472.0022262
X-RAY DIFFRACTIONr_angle_other_deg0.6653.0013874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0815211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.86126.40664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96915318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.43153
X-RAY DIFFRACTIONr_chiral_restr0.0540.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
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: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 66 -
Rwork0.236 1294 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -0.7244 Å / Origin y: 27.655 Å / Origin z: -1.3995 Å
111213212223313233
T0.0105 Å20.0321 Å20.0031 Å2-0.1879 Å20.0196 Å2--0.1999 Å2
L1.3421 °20.0386 °2-0.94 °2-0.692 °20.3195 °2--1.6126 °2
S0.0269 Å °0.3125 Å °0.1315 Å °0.0585 Å °0.1219 Å °-0.0661 Å °-0.0123 Å °-0.0641 Å °-0.1487 Å °

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