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- PDB-1tp9: PRX D (type II) from Populus tremula -

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Basic information

Entry
Database: PDB / ID: 1tp9
TitlePRX D (type II) from Populus tremula
Componentsperoxiredoxin
KeywordsOXIDOREDUCTASE / peroxiredoxin / oligomer / thioredoxin fold
Function / homology
Function and homology information


glutaredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / cellular response to oxidative stress / cytoplasm
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
Peroxiredoxin-2 / Glutaredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsEchalier, A. / Trivelli, X. / Corbier, C. / Rouhier, N. / Walker, O. / Tsan, P. / Jacquot, J.P. / Krimm, I. / Lancelin, J.M.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal structure and solution NMR dynamics of a D (type II) peroxiredoxin glutaredoxin and thioredoxin dependent: a new insight into the peroxiredoxin oligomerism
Authors: Echalier, A. / Trivelli, X. / Corbier, C. / Rouhier, N. / Walker, O. / Tsan, P. / Jacquot, J.P. / Aubry, A. / Krimm, I. / Lancelin, J.M.
History
DepositionJun 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: peroxiredoxin
B: peroxiredoxin
C: peroxiredoxin
D: peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0006
Polymers69,8084
Non-polymers1922
Water11,205622
1
A: peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5482
Polymers17,4521
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5482
Polymers17,4521
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)17,4521
Polymers17,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)17,4521
Polymers17,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.513, 69.112, 76.429
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
peroxiredoxin / Prx D (type II)


Mass: 17452.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Plasmid: pET3d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8S3L0, UniProt: A9PCL4*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.22 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.948 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 3, 2001
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 1.62→29.88 Å / Num. obs: 79011 / % possible obs: 96.14 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.62→1.68 Å / % possible all: 83.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→29.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.946 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22448 7560 10 %RANDOM
Rwork0.18914 ---
all0.19266 79011 --
obs0.19266 68051 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.466 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.51 Å2
2---0.5 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.62→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4895 0 10 622 5527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214987
X-RAY DIFFRACTIONr_bond_other_d0.0320.024625
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9816738
X-RAY DIFFRACTIONr_angle_other_deg1.137310826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6985642
X-RAY DIFFRACTIONr_chiral_restr0.1160.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.025514
X-RAY DIFFRACTIONr_gen_planes_other0.030.02922
X-RAY DIFFRACTIONr_nbd_refined0.2320.2921
X-RAY DIFFRACTIONr_nbd_other0.250.25095
X-RAY DIFFRACTIONr_nbtor_other0.0830.22673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2375
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3540.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2770.234
X-RAY DIFFRACTIONr_mcbond_it1.0841.53197
X-RAY DIFFRACTIONr_mcangle_it1.81925117
X-RAY DIFFRACTIONr_scbond_it2.64731790
X-RAY DIFFRACTIONr_scangle_it4.2444.51621
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.25 457
Rwork0.206 4433

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