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- PDB-2yzh: Crystal structure of peroxiredoxin-like protein from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 2yzh
TitleCrystal structure of peroxiredoxin-like protein from Aquifex aeolicus
ComponentsProbable thiol peroxidase
KeywordsOXIDOREDUCTASE / Redox protein / Antioxidant / Peroxidase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity
Similarity search - Function
Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsEbihara, A. / Manzoku, M. / Fujimoto, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Crystal structure of peroxiredoxin-like protein from Aquifex aeolicus
Authors: Ebihara, A. / Manzoku, M. / Fujimoto, Y. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Probable thiol peroxidase
B: Probable thiol peroxidase
C: Probable thiol peroxidase
D: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5358
Polymers75,1514
Non-polymers3844
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560.2 Å2
MethodPISA
2
A: Probable thiol peroxidase
C: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7684
Polymers37,5752
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1244.9 Å2
MethodPISA
3
B: Probable thiol peroxidase
D: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7684
Polymers37,5752
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240.7 Å2
MethodPISA
4
A: Probable thiol peroxidase
D: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7684
Polymers37,5752
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2081.4 Å2
MethodPISA
5
B: Probable thiol peroxidase
C: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7684
Polymers37,5752
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080.7 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.118, 81.642, 70.909
Angle α, β, γ (deg.)90.00, 105.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable thiol peroxidase / peroxiredoxin-like protein


Mass: 18787.725 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: O66780, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M Magnesium sulfate, 0.1M tri-Sodium citrate pH4.2, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 5, 2007
RadiationMonochromator: SI Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 56115 / % possible obs: 99.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 19.48
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 3.46 / % possible all: 94.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PSQ

1psq


Resolution: 1.85→47.21 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1462349.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.222 5690 10.2 %RANDOM
Rwork0.192 ---
obs0.192 56037 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.795 Å2 / ksol: 0.374831 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å20 Å2-3.44 Å2
2--5.16 Å20 Å2
3----2.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.85→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5230 0 20 371 5621
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 946 10.4 %
Rwork0.233 8109 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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