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- PDB-1e2y: Tryparedoxin peroxidase from Crithidia fasciculata -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1e2y
TitleTryparedoxin peroxidase from Crithidia fasciculata
ComponentsTRYPAREDOXIN PEROXIDASE
KeywordsOXIDOREDUCTASE / 2-CYS PEROXIREDOXIN
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cellular response to stress / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol
Similarity search - Function
Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
thioredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesCRITHIDIA FASCICULATA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsAlphey, M.S. / Bond, C.S. / Hunter, W.N.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The Structure of Reduced Tryparedoxin Peroxidase Reveals a Decamer and Insight Into Reactivity of 2Cys-Peroxiredoxins
Authors: Alphey, M.S. / Bond, C.S. / Tetaud, E. / Fairlamb, A.H. / Hunter, W.N.
History
DepositionMay 30, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: TRYPAREDOXIN PEROXIDASE
B: TRYPAREDOXIN PEROXIDASE
C: TRYPAREDOXIN PEROXIDASE
D: TRYPAREDOXIN PEROXIDASE
E: TRYPAREDOXIN PEROXIDASE
F: TRYPAREDOXIN PEROXIDASE
G: TRYPAREDOXIN PEROXIDASE
H: TRYPAREDOXIN PEROXIDASE
I: TRYPAREDOXIN PEROXIDASE
J: TRYPAREDOXIN PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,48820
Polymers213,13410
Non-polymers35510
Water39622
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19880 Å2
ΔGint-226.59 kcal/mol
Surface area67530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.800, 97.200, 133.800
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.30688, 0.40048, 0.86339), (-0.31193, 0.89938, -0.3063), (-0.89918, -0.17532, 0.40093)-43.37218, 57.19762, 131.65608
2given(-0.79908, 0.3248, 0.50593), (-0.09331, 0.76432, -0.63805), (-0.59393, -0.55706, -0.58045)77.52654, 76.39287, 215.4958
3given(-0.80562, -0.15994, -0.57044), (0.27859, 0.74748, -0.60304), (0.52284, -0.64474, -0.55762)196.63828, 45.45707, 131.04214
4given(0.32192, -0.33853, -0.88418), (0.40605, 0.89301, -0.19407), (0.85527, -0.29654, 0.42494)146.92734, -8.48359, -0.79172

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Components

#1: Protein
TRYPAREDOXIN PEROXIDASE / TRYP


Mass: 21313.393 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRITHIDIA FASCICULATA (eukaryote)
Description: PLASMID TRANSFORMED INTO E. COLI BL21(DE3) STRAIN FOR RECOMBINANT PROTEIN EXPRESSION
Cellular location: CYTOPLASM / Gene: CF-TRYP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9TZX2
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN CRYSTALLIZED FROM 12.5% PEG 1000, 100MM TRIS-HCL PH HANGING DROP CONSISITED
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of 2.5 micro litter of protein mixed with 2 micro litter of reservoir solution and 0.5 micro litter EDTA
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
20.1 MEDTA1drop
312.5 %(w/v)PEG10001reservoir
4100 mMTris-HCl1reservoir
510 %(v/v)glycerol1reservoir
6100 mMdithiothreitol1reservoir
70.25 %(v/v)DMSO1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8800,0.9790,0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 1999 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.881
20.9791
30.97921
ReflectionResolution: 3.2→21 Å / Num. obs: 52094 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 56.4 Å2 / Rsym value: 0.091 / Net I/σ(I): 14.8
Reflection shellResolution: 3.2→21 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.48 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 376643 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.48

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.2→21 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2625 5 %RANDOM
Rwork0.273 ---
obs0.273 52094 98.95 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 12.362 Å2 / ksol: 0.205 e/Å3
Displacement parametersBiso mean: 71 Å2
Baniso -1Baniso -2Baniso -3
1-13.84 Å20 Å25.53 Å2
2---21.76 Å20 Å2
3---7.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 3.2→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13179 0 10 22 13211
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.43
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.41
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3.2→3.31 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.48 175 5 %
Rwork0.41 4866 -
obs--96.6 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.41
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15

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