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- PDB-2yjh: Thiol Peroxidase from Yersinia Psuedotuberculosis, inactive mutan... -

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Basic information

Entry
Database: PDB / ID: 2yjh
TitleThiol Peroxidase from Yersinia Psuedotuberculosis, inactive mutant C61S
ComponentsTHIOL PEROXIDASE
KeywordsOXIDOREDUCTASE / ATYPICAL 2-CYS PEROXIREDOXIN / PEROXIDE PROTECTION / ANTI- VIRULENCE
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 speciesYERSINIA PSEUDOTUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBeckham, K.S.H. / Gabrielsen, M. / Wang, D. / Roe, A.J.
CitationJournal: Plos One / Year: 2012
Title: Structural Characterisation of Tpx from Yersinia Pseudotuberculosis Reveals Insights Into the Binding of Salicylidene Acylhydrazide Compounds.
Authors: Gabrielsen, M. / Beckham, K.S.H. / Feher, V.A. / Zetterstrom, C.E. / Wang, D. / Muller, S. / Elofsson, M. / Amaro, R.E. / Byron, O. / Roe, A.J.
History
DepositionMay 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Source and taxonomy
Revision 1.2Mar 4, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: THIOL PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)21,3811
Polymers21,3811
Non-polymers00
Water724
1
A: THIOL PEROXIDASE

A: THIOL PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)42,7622
Polymers42,7622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area1510 Å2
ΔGint-13 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.030, 65.030, 85.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein THIOL PEROXIDASE


Mass: 21381.211 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) / Strain: PIB102 / Plasmid: PET-151 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q66A71, peroxiredoxin, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 61 TO SER

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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: 2.61 Å3/Da / Density % sol: 52.95 % / Description: NONE
Crystal growpH: 7.6 / Details: 12% PEG 3350, 0.05 M NA, HEPES PH 7.0, 1% TRYPTONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 25, 2010 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.55→56.32 Å / Num. obs: 6151 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.6
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 72.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XPD

2xpd


Resolution: 2.55→56.32 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.871 / SU B: 19.246 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R: 0.897 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.33661 296 4.9 %RANDOM
Rwork0.31173 ---
obs0.31286 5803 90.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.083 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å21.23 Å20 Å2
2--2.47 Å20 Å2
3----3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.55→56.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1188 0 0 4 1192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221204
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7721.9691641
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4725164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23425.22744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89715184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.226155
X-RAY DIFFRACTIONr_chiral_restr0.0430.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021896
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1441.5816
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.25721305
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.0143388
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.0214.5336
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.551→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 25 -
Rwork0.39 482 -
obs--99.22 %

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