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- PDB-5k1g: Crystal structure of reduced Prx3 from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 5k1g
TitleCrystal structure of reduced Prx3 from Vibrio vulnificus
Components1-Cys peroxiredoxin
KeywordsOXIDOREDUCTASE / 1-Cys Prx / Vibrio vulnificus / hydrogen peroxide / nitric oxide
Function / homology
Function and homology information


glutathione-dependent peroxiredoxin / thioredoxin peroxidase activity / cellular response to oxidative stress
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutathione-dependent peroxiredoxin
Similarity search - Component
Biological speciesVibrio vulnificus MO6-24/O (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsAhn, J. / Ha, N.-C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry for Food, Agriculture, Forestry and Fisheries Korea, Republic Of
CitationJournal: IUCrJ / Year: 2018
Title: Crystal structure of peroxiredoxin 3 fromVibrio vulnificusand its implications for scavenging peroxides and nitric oxide.
Authors: Ahn, J. / Jang, K.K. / Jo, I. / Nurhasni, H. / Lim, J.G. / Yoo, J.W. / Choi, S.H. / Ha, N.C.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-Cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)17,5461
Polymers17,5461
Non-polymers00
Water66737
1
A: 1-Cys peroxiredoxin

A: 1-Cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)35,0922
Polymers35,0922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_766-x+2,-x+y+1,-z+5/31
Buried area1340 Å2
ΔGint-9 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.871, 73.871, 62.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

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Components

#1: Protein 1-Cys peroxiredoxin


Mass: 17545.971 Da / Num. of mol.: 1 / Mutation: C48D, C73S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus MO6-24/O (bacteria) / Strain: MO6-24/O / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Z0YU25*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe reference database is GenBank ADV89163. This protein is C48D/C73S mutant, and residues 158-164 ...The reference database is GenBank ADV89163. This protein is C48D/C73S mutant, and residues 158-164 are expression tag.

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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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.8 M sodium acetate, 0.1 M Tris-HCl, 0.2M sodium chloride
PH range: 6.0-6.8

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Data collection

DiffractionMean temperature: 100.15 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2015
RadiationMonochromator: Double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.899→50 Å / Num. obs: 15873 / % possible obs: 99.3 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 4.57
Reflection shellResolution: 1.9→1.93 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F82

4f82


Resolution: 1.899→31.987 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 1471 9.95 %
Rwork0.2202 --
obs0.224 14790 93.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→31.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 0 37 1189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021171
X-RAY DIFFRACTIONf_angle_d0.5741591
X-RAY DIFFRACTIONf_dihedral_angle_d12.856698
X-RAY DIFFRACTIONf_chiral_restr0.044192
X-RAY DIFFRACTIONf_plane_restr0.004205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8988-1.96010.3122710.2478713X-RAY DIFFRACTION56
1.9601-2.03010.37841100.28691028X-RAY DIFFRACTION80
2.0301-2.11140.28021340.25591201X-RAY DIFFRACTION94
2.1114-2.20750.29791420.25371253X-RAY DIFFRACTION99
2.2075-2.32380.291420.24331283X-RAY DIFFRACTION100
2.3238-2.46930.32151470.24221282X-RAY DIFFRACTION100
2.4693-2.65990.25981410.23261286X-RAY DIFFRACTION100
2.6599-2.92740.2781430.23581307X-RAY DIFFRACTION100
2.9274-3.35060.25741460.22431298X-RAY DIFFRACTION100
3.3506-4.21990.20861430.19341316X-RAY DIFFRACTION100
4.2199-31.99160.20361520.17171352X-RAY DIFFRACTION98

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