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- PDB-5y63: Crystal structure of Enterococcus faecalis AhpC -

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Basic information

Entry
Database: PDB / ID: 5y63
TitleCrystal structure of Enterococcus faecalis AhpC
ComponentsAlkyl hydroperoxide reductase, C subunit
KeywordsOXIDOREDUCTASE / 2Cys peroxiredoxins
Function / homology
Function and homology information


NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / peroxiredoxin activity / peroxidase activity / response to oxidative stress / cytoplasm
Similarity search - Function
Alkyl hydroperoxide reductase subunit C / Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Alkyl hydroperoxide reductase subunit C / Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alkyl hydroperoxide reductase C
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsPan, A. / Balakrishna, A.M. / Grueber, G.
CitationJournal: Free Radic. Biol. Med. / Year: 2017
Title: Atomic structure and enzymatic insights into the vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit C
Authors: Pan, A. / Balakrishna, A.M. / Nartey, W. / Kohlmeier, A. / Dip, P.V. / Bhushan, S. / Gruber, G.
History
DepositionAug 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkyl hydroperoxide reductase, C subunit
B: Alkyl hydroperoxide reductase, C subunit
C: Alkyl hydroperoxide reductase, C subunit
D: Alkyl hydroperoxide reductase, C subunit
E: Alkyl hydroperoxide reductase, C subunit


Theoretical massNumber of molelcules
Total (without water)104,8725
Polymers104,8725
Non-polymers00
Water2,432135
1
A: Alkyl hydroperoxide reductase, C subunit
B: Alkyl hydroperoxide reductase, C subunit
C: Alkyl hydroperoxide reductase, C subunit
D: Alkyl hydroperoxide reductase, C subunit
E: Alkyl hydroperoxide reductase, C subunit

A: Alkyl hydroperoxide reductase, C subunit
B: Alkyl hydroperoxide reductase, C subunit
C: Alkyl hydroperoxide reductase, C subunit
D: Alkyl hydroperoxide reductase, C subunit
E: Alkyl hydroperoxide reductase, C subunit


Theoretical massNumber of molelcules
Total (without water)209,74510
Polymers209,74510
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)103.191, 124.674, 97.788
Angle α, β, γ (deg.)90.00, 113.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

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Components

#1: Protein
Alkyl hydroperoxide reductase, C subunit


Mass: 20974.455 Da / Num. of mol.: 5 / Fragment: UNP residues 1-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria)
Strain: ATCC 700802 / V583 / Gene: ahpC, EF_2739 / Plasmid: pET-9d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H7C7A0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris HCl pH 8.5, Magnesium Chloride, PEG 400 (30%)

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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 16, 2015 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 25934 / % possible obs: 99.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 56.23 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.6
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.765 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O5R

4o5r


Resolution: 2.87→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.902 / SU B: 38.752 / SU ML: 0.328 / Cross valid method: THROUGHOUT / ESU R Free: 0.389 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25171 1297 5.1 %RANDOM
Rwork0.20774 ---
obs0.21001 24376 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.494 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å2-1.14 Å2
2--4.81 Å20 Å2
3----3.29 Å2
Refinement stepCycle: 1 / Resolution: 2.87→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6655 0 0 135 6790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0196828
X-RAY DIFFRACTIONr_bond_other_d0.0010.026107
X-RAY DIFFRACTIONr_angle_refined_deg0.7861.9359233
X-RAY DIFFRACTIONr_angle_other_deg0.649314104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7025827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71524.795365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.438151104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4531525
X-RAY DIFFRACTIONr_chiral_restr0.0490.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021649
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_it1.135.1083323
X-RAY DIFFRACTIONr_mcbond_other1.1295.1063322
X-RAY DIFFRACTIONr_mcangle_it2.097.6434145
X-RAY DIFFRACTIONr_mcangle_other2.0897.6464146
X-RAY DIFFRACTIONr_scbond_it0.8085.1273505
X-RAY DIFFRACTIONr_scbond_other0.8085.1293506
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4977.675089
X-RAY DIFFRACTIONr_long_range_B_refined3.6840.1917839
X-RAY DIFFRACTIONr_long_range_B_other3.66540.2027822
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.865→2.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 68 -
Rwork0.291 1536 -
obs--85.5 %
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)
10.5863-0.4080.60311.3392-0.70442.27480.14840.1037-0.043-0.0343-0.012-0.14420.24650.1095-0.13640.05010.0293-0.02630.0368-0.06050.1591-18.5766-36.212827.3817
20.71570.19480.2551.8453-0.92492.48210.0558-0.0257-0.0313-0.19660.1110.14420.0416-0.0852-0.16680.0344-0.0139-0.01860.0387-0.02640.0658-39.5405-23.486918.1006
30.4990.47570.14462.71120.33121.0694-0.055-0.07910.0659-0.41840.063-0.10280.10250.0562-0.0080.09230.00580.02470.0452-0.00710.0315-28.43765.71343.0711
40.31750.19780.55962.30560.42861.0938-0.0579-0.08640.0609-0.1067-0.09020.1853-0.0749-0.14330.14810.02580.0333-0.00720.08210.00830.0686-40.44725.765815.048
51.07580.22530.70911.05540.20692.4682-0.09190.05830.0487-0.10420.03030.0421-0.17030.12670.06160.0209-0.0089-0.00440.02310.03650.0748-16.390444.030931.9328
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 167
2X-RAY DIFFRACTION2B1 - 166
3X-RAY DIFFRACTION3C1 - 167
4X-RAY DIFFRACTION4D1 - 167
5X-RAY DIFFRACTION5E1 - 165

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