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- PDB-6ky4: Crystal structure of Sulfiredoxin from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 6ky4
TitleCrystal structure of Sulfiredoxin from Arabidopsis thaliana
ComponentsSulfiredoxin, chloroplastic/mitochondrial
KeywordsOXIDOREDUCTASE / sulfiredoxin / cysteine / sulfinic acid / peroxiredoxin repair protein / arabidopsis thaliana / antioxidant
Function / homology
Function and homology information


sulfiredoxin / sulfiredoxin activity / chloroplast / cellular response to oxidative stress / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Sulfiredoxin / ParB N-terminal domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Sulfiredoxin, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLiu, M. / Wang, J. / Li, X. / Li, M. / Sylvanno, M.J. / Zhang, M. / Wang, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: The crystal structure of sulfiredoxin from Arabidopsis thaliana revealed a more robust antioxidant mechanism in plants.
Authors: Liu, M. / Wang, J. / Li, X. / Sylvanno, M.J. / Li, M. / Zhang, M. / Wang, M.
History
DepositionSep 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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: Sulfiredoxin, chloroplastic/mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3874
Polymers12,7701
Non-polymers6173
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-11 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.544, 102.544, 102.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Sulfiredoxin, chloroplastic/mitochondrial / AtSRX


Mass: 12769.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SRX, At1g31170, F28K20.12 / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8GY89, sulfiredoxin
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.8 M NaH2PO4/1.2 M KH2PO4, acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 3377 / % possible obs: 99.9 % / Redundancy: 37 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.018 / Rrim(I) all: 0.099 / Χ2: 1.054 / Net I/σ(I): 12 / Num. measured all: 124863
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.3137.22.2613300.8510.3722.2920.908100
3.31-3.4543.11.2483180.9460.1911.2631.094100
3.45-3.642.80.6683290.9830.1030.6771.055100
3.6-3.7941.40.3813230.990.060.3861.125100
3.79-4.0339.50.2593260.9960.0420.2621.258100
4.03-4.3438.50.1483290.9990.0240.151.055100
4.34-4.7833.80.13330.9990.0170.1010.976100
4.78-5.4736.20.093430.9990.0150.0911.029100
5.47-6.8935.20.0753510.9990.0130.0760.984100
6.89-5024.90.0733950.9980.0150.0741.02699

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xw3

1xw3


Resolution: 3.2→41.863 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.56
RfactorNum. reflection% reflection
Rfree0.2938 334 10.01 %
Rwork0.2443 --
obs0.2492 3335 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.52 Å2 / Biso mean: 66.2696 Å2 / Biso min: 38.51 Å2
Refinement stepCycle: final / Resolution: 3.2→41.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 37 4 771
Biso mean--70.73 49.16 -
Num. residues----89
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.2-4.03480.33141610.28941448
4.0348-41.860.27541730.22241553

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