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- PDB-2p5r: Crystal structure of the poplar glutathione peroxidase 5 in the o... -

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Basic information

Entry
Database: PDB / ID: 2p5r
TitleCrystal structure of the poplar glutathione peroxidase 5 in the oxidized form
ComponentsGlutathione peroxidase 5
KeywordsOXIDOREDUCTASE / Thioredoxin fold
Function / homology
Function and homology information


glutathione peroxidase activity / response to oxidative stress / metal ion binding
Similarity search - Function
Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutathione peroxidase
Similarity search - Component
Biological speciesPopulus trichocarpa x Populus deltoides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKoh, C.S. / Didierjean, C. / Navrot, N. / Panjikar, S. / Mulliert, G. / Rouhier, N. / Jacquot, J.-P. / Aubry, A. / Shawkataly, O. / Corbier, C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of a Poplar Thioredoxin Peroxidase that Exhibits the Structure of Glutathione Peroxidases: Insights into Redox-driven Conformational Changes.
Authors: Koh, C.S. / Didierjean, C. / Navrot, N. / Panjikar, S. / Mulliert, G. / Rouhier, N. / Jacquot, J.P. / Aubry, A. / Shawkataly, O. / Corbier, C.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione peroxidase 5
B: Glutathione peroxidase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0667
Polymers38,8662
Non-polymers2005
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.580, 71.580, 117.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Glutathione peroxidase 5 /


Mass: 19432.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa x Populus deltoides (plant)
Gene: PtGPX5 / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pSBET
References: UniProt: A3FNZ8, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 25 % PEG 4000, 0.1 M Tris-HCl, 0.2 M calcium chloride, pH 8.5, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.8063 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8063 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 13374 / Num. obs: 13374 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.062 / Χ2: 0.275 / Net I/σ(I): 6.2
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 7.79 % / Rmerge(I) obs: 0.335 / Num. unique all: 654 / Χ2: 0.181 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1325 9.9 %RANDOM
Rwork0.211 ---
all0.218 12907 --
obs0.218 12907 96.6 %-
Solvent computationBsol: 43.036 Å2
Displacement parametersBiso mean: 46.066 Å2
Baniso -1Baniso -2Baniso -3
1--4.223 Å2-6.459 Å20 Å2
2---4.223 Å20 Å2
3---8.446 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 0 5 224 2879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061.5
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d23.92
X-RAY DIFFRACTIONc_improper_angle_d0.722.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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