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- PDB-5k2j: Crystal structure of reduced Prx3 in complex with h2o2 from Vibri... -

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Basic information

Entry
Database: PDB / ID: 5k2j
TitleCrystal structure of reduced Prx3 in complex with h2o2 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
HYDROGEN PEROXIDE / Glutathione-dependent peroxiredoxin
Similarity search - Component
Biological speciesVibrio vulnificus MO6-24/O (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.908 Å
AuthorsAhn, J. / Ha, N.-C.
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 19, 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

Downloads & links

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Assembly

Deposited unit
A: 1-Cys peroxiredoxin
B: 1-Cys peroxiredoxin
C: 1-Cys peroxiredoxin
D: 1-Cys peroxiredoxin
E: 1-Cys peroxiredoxin
F: 1-Cys peroxiredoxin
G: 1-Cys peroxiredoxin
H: 1-Cys peroxiredoxin
I: 1-Cys peroxiredoxin
J: 1-Cys peroxiredoxin
K: 1-Cys peroxiredoxin
L: 1-Cys peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,68816
Polymers210,55212
Non-polymers1364
Water14,502805
1
A: 1-Cys peroxiredoxin
B: 1-Cys peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1263
Polymers35,0922
Non-polymers341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-9 kcal/mol
Surface area13880 Å2
MethodPISA
2
C: 1-Cys peroxiredoxin
D: 1-Cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)35,0922
Polymers35,0922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-11 kcal/mol
Surface area13700 Å2
MethodPISA
3
E: 1-Cys peroxiredoxin
F: 1-Cys peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1263
Polymers35,0922
Non-polymers341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-9 kcal/mol
Surface area13450 Å2
MethodPISA
4
G: 1-Cys peroxiredoxin
H: 1-Cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)35,0922
Polymers35,0922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-10 kcal/mol
Surface area12920 Å2
MethodPISA
5
I: 1-Cys peroxiredoxin
J: 1-Cys peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1263
Polymers35,0922
Non-polymers341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-10 kcal/mol
Surface area13080 Å2
MethodPISA
6
K: 1-Cys peroxiredoxin
L: 1-Cys peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1263
Polymers35,0922
Non-polymers341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-9 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.080, 97.725, 97.492
Angle α, β, γ (deg.)78.72, 67.33, 67.34
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
1-Cys peroxiredoxin


Mass: 17545.971 Da / Num. of mol.: 12 / 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: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 805 / 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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.8 M sodium citrate, 0.1 M Tris-HCl, 0.2 M sodium chloride, 500 uM H2O2
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: Oct 20, 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: 1.9→50 Å / Num. obs: 182028 / % possible obs: 90 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.5
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: 5K1G

5k1g


Resolution: 1.908→19.68 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2.22 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 6747 4.92 %
Rwork0.1946 --
obs0.197 137002 74.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.908→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14143 0 8 805 14956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314397
X-RAY DIFFRACTIONf_angle_d0.57219543
X-RAY DIFFRACTIONf_dihedral_angle_d12.918572
X-RAY DIFFRACTIONf_chiral_restr0.0462330
X-RAY DIFFRACTIONf_plane_restr0.0042522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9079-1.92960.2801780.231058X-RAY DIFFRACTION19
1.9296-1.95230.3503600.23021224X-RAY DIFFRACTION21
1.9523-1.97610.3166670.22291278X-RAY DIFFRACTION22
1.9761-2.00110.2732880.24131561X-RAY DIFFRACTION27
2.0011-2.02740.3294910.23531879X-RAY DIFFRACTION32
2.0274-2.05510.24951010.23072176X-RAY DIFFRACTION38
2.0551-2.08440.29681250.24392587X-RAY DIFFRACTION44
2.0844-2.11550.32591490.25423024X-RAY DIFFRACTION52
2.1155-2.14850.31212090.25033488X-RAY DIFFRACTION61
2.1485-2.18370.27812290.2423829X-RAY DIFFRACTION66
2.1837-2.22130.27312340.23094181X-RAY DIFFRACTION71
2.2213-2.26170.3072640.24655248X-RAY DIFFRACTION91
2.2617-2.30510.31361960.22714776X-RAY DIFFRACTION83
2.3051-2.35210.2962620.23224979X-RAY DIFFRACTION85
2.3521-2.40310.28312710.23045180X-RAY DIFFRACTION89
2.4031-2.45890.26882840.22295354X-RAY DIFFRACTION92
2.4589-2.52030.28542950.22045469X-RAY DIFFRACTION94
2.5203-2.58830.26672930.20615431X-RAY DIFFRACTION94
2.5883-2.66430.27083120.21065516X-RAY DIFFRACTION95
2.6643-2.75010.27872930.21375523X-RAY DIFFRACTION96
2.7501-2.84810.25213150.22655609X-RAY DIFFRACTION97
2.8481-2.96170.25142470.21655770X-RAY DIFFRACTION97
2.9617-3.0960.27523120.20635592X-RAY DIFFRACTION98
3.096-3.25860.24443480.20125700X-RAY DIFFRACTION98
3.2586-3.46170.2293020.18645638X-RAY DIFFRACTION98
3.4617-3.72730.20912900.175762X-RAY DIFFRACTION98
3.7273-4.09940.20052960.15995668X-RAY DIFFRACTION98
4.0994-4.68560.17522200.13525586X-RAY DIFFRACTION95
4.6856-5.87710.18282800.14465617X-RAY DIFFRACTION97
5.8771-19.68130.20722360.17425552X-RAY DIFFRACTION94

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