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- PDB-2pwj: Structure of a mitochondrial type II peroxiredoxin from Pisum sativum -

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Basic information

Entry
Database: PDB / ID: 2pwj
TitleStructure of a mitochondrial type II peroxiredoxin from Pisum sativum
ComponentsMitochondrial peroxiredoxin
KeywordsOXIDOREDUCTASE / alpha and beta protein
Function / homology
Function and homology information


glutaredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / cellular response to oxidative stress / mitochondrion
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
Glutaredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLopez-Jaramillo, F.J. / Barranco-Medina, S. / Lazaro, J.J. / Santoyo-Gonzalez, F.
Citation
Journal: To be Published
Title: Structure of a mitochondrial type II peroxiredoxin from Pisum sativum
Authors: Lopez-Jaramillo, F.J. / Barranco-Medina, S. / Lazaro, J.J. / Santoyo-Gonzalez, F.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Cloning, overexpression, purification and preliminary crystallographic studies of a mitochondrial type II peroxiredoxin from Pisum sativum
Authors: Barranco-Medina, S. / Lopez-Jaramillo, F.J. / Bernier-Villamor, L. / Sevilla, F. / Lazaro, J.J.
History
DepositionMay 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Mitochondrial peroxiredoxin
B: Mitochondrial peroxiredoxin
C: Mitochondrial peroxiredoxin
D: Mitochondrial peroxiredoxin
E: Mitochondrial peroxiredoxin
F: Mitochondrial peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)110,7896
Polymers110,7896
Non-polymers00
Water00
1
A: Mitochondrial peroxiredoxin
C: Mitochondrial peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)36,9302
Polymers36,9302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitochondrial peroxiredoxin
F: Mitochondrial peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)36,9302
Polymers36,9302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Mitochondrial peroxiredoxin
E: Mitochondrial peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)36,9302
Polymers36,9302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.880, 66.400, 77.230
Angle α, β, γ (deg.)102.94, 104.44, 99.07
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly seems to be a dimer althoug hexameric forms have been detected. This point is beind elucidated by biochemical experiments and analysis of this structure

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Components

#1: Protein
Mitochondrial peroxiredoxin


Mass: 18464.836 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: prx / Plasmid: pET3d_Prx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6KBB1, peroxiredoxin

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG2000, citrate, NaCl, DTT, 2-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418
DetectorType: BRUKER PLATINUM 200 / Detector: CCD / Date: Feb 2, 2005 / Details: Microstar micro-focus
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.39→71.9 Å / Num. all: 30073 / Num. obs: 30073 / % possible obs: 65.79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.08 % / Biso Wilson estimate: 22.1 Å2 / Limit h max: 20 / Limit h min: -24 / Limit k max: 25 / Limit k min: -24 / Limit l max: 31 / Limit l min: 0 / Observed criterion F max: 1058698.45 / Observed criterion F min: 1.31 / Rsym value: 0.067 / Net I/σ(I): 15.416
Reflection shell
Resolution (Å)Highest resolution (Å)Rsym value
2.4-2.480.078
2.48-2.580.103
2.58-2.70.094
2.7-2.840.092
2.84-3.020.083
3.02-3.260.073
3.26-3.580.067
3.58-4.10.066
4.1-5.170.065
5.170.063

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Phasing

Phasing MRRfactor: 0.613 / Cor.coef. Fo:Fc: 0.3 / Cor.coef. Io to Ic: 0.231
Highest resolutionLowest resolution
Rotation2.7 Å8 Å
Translation2.7 Å8 Å

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Processing

Software
NameVersionClassificationNB
SAINTV7.12Adata scaling
AMoREphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model generated by EasyPed3D Web Server 1.0

Resolution: 2.8→14.98 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 7476 Nonpolymer 0 Solvent 0 CNS ...Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 7476 Nonpolymer 0 Solvent 0 CNS Parameter files: CNS_TOPPAR/protein_rep.param CNS_TOPPAR/carbohydrate.param CNS Topology files: CNS_TOPPAR/protein.top CNS_TOPPAR/carbohydrate.top
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2544 9.9 %RANDOM
Rwork0.277 ---
all0.298 27653 --
obs0.298 25728 93 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 14.9103 Å2 / ksol: 0.296614 e/Å3
Displacement parametersBiso max: 39.46 Å2 / Biso mean: 14.29 Å2 / Biso min: 5.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.53 Å2-4.01 Å25.77 Å2
2---5.66 Å2-0.18 Å2
3----1.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.53 Å
Luzzati d res high-2.8
Refinement stepCycle: LAST / Resolution: 2.8→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7476 0 0 0 7476
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_torsion_deg23.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.93
X-RAY DIFFRACTIONx_mcbond_it0.971.5
X-RAY DIFFRACTIONx_mcangle_it1.652
X-RAY DIFFRACTIONx_scbond_it1.412
X-RAY DIFFRACTIONx_scangle_it2.172.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.8-2.930.39925110.90.38820620.0253471231366.6
2.93-3.080.382669.10.34626690.0233465293584.7
3.08-3.270.341341100.32630560.0183451339798.4
3.27-3.520.333269.50.30930990.0183447342599.4
3.52-3.870.293179.20.27731240.0163471344199.1
3.87-4.420.249343100.23130800.0133464342398.8
4.42-5.520.25534910.20.23130680.0143459341798.8
5.52-14.980.23235110.40.24230260.0123452337797.8

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