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- PDB-2xpd: Reduced Thiol peroxidase (Tpx) from yersinia Pseudotuberculosis -

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Basic information

Entry
Database: PDB / ID: 2xpd
TitleReduced Thiol peroxidase (Tpx) from yersinia Pseudotuberculosis
ComponentsTHIOL PEROXIDASE
KeywordsOXIDOREDUCTASE / PEROXIREDOXIN / THIOREDOXIN-FOLD / ROS PROTECTION
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 / Thioredoxin-like superfamily ...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
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Thiol peroxidase / Thiol peroxidase
Similarity search - Component
Biological speciesYERSINIA PSEUDOTUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGabrielsen, M. / Zetterstrom, C.E. / Wang, D. / Elofsson, M. / Roe, A.J.
Citation
Journal: 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. / Feher, V.A. / Zetterstrom, C.E. / Wang, D. / Muller, S. / Elofsson, M. / Amaro, R.E. / Byron, O. / Roe, A.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Expression, Purification, Crystallization and Initial X-Ray Diffraction Analysis of Thiol Peroxidase from Yersinia Pseudotuberculosis.
Authors: Gabrielsen, M. / Zetterstrom, C.E. / Wang, D. / Beckham, K.S. / Elofsson, M. / Isaacs, N.W. / Roe, A.J.
History
DepositionAug 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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: THIOL PEROXIDASE
B: THIOL PEROXIDASE
C: THIOL PEROXIDASE
D: THIOL PEROXIDASE
E: THIOL PEROXIDASE
F: THIOL PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5387
Polymers128,3846
Non-polymers1541
Water8,971498
1
A: THIOL PEROXIDASE
B: THIOL PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9493
Polymers42,7952
Non-polymers1541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-18.4 kcal/mol
Surface area13450 Å2
MethodPISA
2
E: THIOL PEROXIDASE
F: THIOL PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)42,7952
Polymers42,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-11.9 kcal/mol
Surface area13180 Å2
MethodPISA
3
C: THIOL PEROXIDASE
D: THIOL PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)42,7952
Polymers42,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-11.1 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.865, 92.068, 85.605
Angle α, β, γ (deg.)90.00, 91.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
THIOL PEROXIDASE


Mass: 21397.277 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) / Strain: YPIII / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q66A71, UniProt: A0A0H3B2F9*PLUS, peroxiredoxin
#2: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE INCLUDES THE NON-CLEAVED HIS6-TAG AND THE TEV PROTEASE RECOGNITION SITE.

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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: 2.42 Å3/Da / Density % sol: 49.23 % / Description: NONE
Crystal growpH: 7.5
Details: 20% PEG 3 350, 0.2 M SODIUM CITRATE TRIBASIC, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2010 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→44.67 Å / Num. obs: 64433 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 5.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.7 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODIFIED PDB ENTRY 3HVV

3hvv


Resolution: 2→44.668 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.882 / SU B: 12.258 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 3285 5.1 %RANDOM
Rwork0.2222 ---
obs0.225 64411 94.742 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.874 Å2
Baniso -1Baniso -2Baniso -3
1--0.419 Å20 Å20.103 Å2
2---0.508 Å20 Å2
3---0.932 Å2
Refinement stepCycle: LAST / Resolution: 2→44.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7340 0 8 498 7846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0227474
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9710167
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60551000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81725.278288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.933151191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5481532
X-RAY DIFFRACTIONr_chiral_restr0.130.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215555
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.23472
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.25207
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2486
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5551.54971
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6827972
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.16132503
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9574.52195
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.47137474
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 227 -
Rwork0.32 4319 -
obs--91.029 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7521-0.25250.0990.374-0.03660.16320.00780.02670.0251-0.0217-0.0231-0.0056-0.0103-0.01120.01530.04340.0027-0.00720.061-0.00090.08331.188-6.07222.839
21.0054-0.18180.03920.3621-0.03930.12940.01530.0431-0.0605-0.011-0.02020.00440.00430.01860.00490.04350.0018-0.00910.0573-0.00730.082529.025-17.7722.974
30.27750.0155-0.05410.7513-0.02590.3786-0.0215-0.00270.02670.0140.0034-0.002-0.0357-0.00080.01810.0628-0.0027-0.01570.04850.00040.078514.8543.05451.082
40.52460.06410.04860.70570.08340.2996-0.02620.0052-0.0629-0.00310.00270.01770.0270.00930.02350.0594-0.0050.0090.03980.00080.095115.58-26.97251.334
50.89670.12490.31650.9128-0.12610.51360.0112-0.0160.00260.0111-0.00340.12670.0154-0.0172-0.00780.0555-0.00510.00360.0605-0.00530.07514.256-19.327-5.593
61.55870.4212-0.46892.0316-0.49210.38770.1224-0.1162-0.00420.122-0.1948-0.4042-0.07310.07970.07240.0556-0.0303-0.0340.06640.03670.142830.635-4.741-6.341
75.3327.5751-0.838410.7685-1.18930.13490.0368-0.05-0.06750.0382-0.064-0.0858-0.00750.00730.02720.10480.0199-0.01050.11450.00020.136612.668-24.88430.655
80.0417-0.03120.01980.0293-0.02480.12630.00090.0019-0.0072-0.0022-0.00690.0089-0.00410.00360.0060.0568-0.0068-0.00710.05730.00220.105414.147-12.31626.806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 167
2X-RAY DIFFRACTION2B2 - 167
3X-RAY DIFFRACTION3C-2 - 167
4X-RAY DIFFRACTION4D1 - 167
5X-RAY DIFFRACTION5E1 - 167
6X-RAY DIFFRACTION6F2 - 167
7X-RAY DIFFRACTION7A501
8X-RAY DIFFRACTION8A2001 - 2117
9X-RAY DIFFRACTION8B2001 - 2101
10X-RAY DIFFRACTION8C2001 - 2082
11X-RAY DIFFRACTION8D2001 - 2089
12X-RAY DIFFRACTION8E2001 - 2062
13X-RAY DIFFRACTION8F2001 - 2047

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