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- PDB-4r0t: Crystal structure of P. aeruginosa TpbA (C132S) in complex with pTyr -

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Basic information

Entry
Database: PDB / ID: 4r0t
TitleCrystal structure of P. aeruginosa TpbA (C132S) in complex with pTyr
ComponentsProtein tyrosine phosphatase TpbA
KeywordsHYDROLASE / DUSP fold / protein tyrosine phosphatase
Function / homology
Function and homology information


protein-serine/threonine phosphatase / phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / periplasmic space
Similarity search - Function
Atypical dual-specificity phosphatase Siw14-like / Tyrosine phosphatase family / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / TYROSINE / Dual specificity protein phosphatase TpbA
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsXu, K. / Li, S. / Wang, Y. / Bartlam, M.
CitationJournal: Plos One
Title: Structural and Biochemical Analysis of Tyrosine Phosphatase Related to Biofilm Formation A (TpbA) from the Opportunistic Pathogen Pseudomonas aeruginosa PAO1
Authors: Xu, K. / Li, S. / Yang, W. / Li, K. / Bai, Y. / Xu, Y. / Jin, J. / Wang, Y. / Bartlam, M.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
B: Protein tyrosine phosphatase TpbA
A: Protein tyrosine phosphatase TpbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3545
Polymers47,9832
Non-polymers3713
Water75742
1
B: Protein tyrosine phosphatase TpbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2683
Polymers23,9911
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Protein tyrosine phosphatase TpbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0862
Polymers23,9911
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.835, 82.614, 120.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-422-

HOH

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Components

#1: Protein Protein tyrosine phosphatase TpbA


Mass: 23991.398 Da / Num. of mol.: 2 / Mutation: C132S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: tpbA, PA3885 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXC7
#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15%(w/v) PEG10000, 0.1M citrate, 2%(v/v) dioxane, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 11739 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.6→2.64 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.603→28.517 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 1169 10 %RANDOM
Rwork0.2167 ---
obs0.2215 11694 94.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.15 Å2 / Biso mean: 64.7115 Å2 / Biso min: 23.2 Å2
Refinement stepCycle: LAST / Resolution: 2.603→28.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 22 42 2595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042597
X-RAY DIFFRACTIONf_angle_d0.7393521
X-RAY DIFFRACTIONf_chiral_restr0.033386
X-RAY DIFFRACTIONf_plane_restr0.003467
X-RAY DIFFRACTIONf_dihedral_angle_d13.714959
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6028-2.72120.31831550.27421313146896
2.7212-2.86450.3511530.288413791532100
2.8645-3.04380.33371440.25761360150499
3.0438-3.27850.30451530.25511371152499
3.2785-3.60780.3281520.23671380153299
3.6078-4.12850.27881160.2276990110671
4.1285-5.19640.20361510.17161373152497
5.1964-28.51870.21791450.18631359150492
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)
12.940.1981-0.35673.6482-0.37585.6822-0.0195-0.19370.05040.37150.0729-0.4492-0.02590.2629-0.02110.4290.0508-0.04960.4014-0.04410.2608-18.85334.0229-17.7653
22.7848-0.11391.47052.90420.05153.54740.0795-0.3964-0.53590.3921-0.0030.68570.1439-0.2406-0.06640.4334-0.02410.10770.4180.05760.8321-55.40741.1806-17.4271
32.00012.000122.00012.00012-3.5032-9.1796-0.81322.89662.21070.0317-1.5579-0.37331.32681.1390.5421-0.50351.59620.02291.0389-17.93596.3433-2.5615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND RESID 34 THROUGH 195
2X-RAY DIFFRACTION2CHAIN A AND RESID 34 THROUGH 198
3X-RAY DIFFRACTION3CHAIN B AND RESID 301 THROUGH 301

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