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- PDB-4r0s: Crystal structure of P. aeruginosa TpbA -

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Basic information

Entry
Database: PDB / ID: 4r0s
TitleCrystal structure of P. aeruginosa TpbA
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 / Dual specificity protein phosphatase TpbA
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsXu, K. / Li, S. / Wang, Y. / Bartlam, M.
CitationJournal: PLoS ONE / Year: 2015
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 1.1Nov 22, 2017Group: Database references / Refinement description / Category: citation / software / Item: _citation.journal_abbrev / _citation.year
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Protein tyrosine phosphatase TpbA
B: Protein tyrosine phosphatase TpbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2975
Polymers48,0152
Non-polymers2823
Water45025
1
A: Protein tyrosine phosphatase TpbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1022
Polymers24,0071
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein tyrosine phosphatase TpbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1953
Polymers24,0071
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.138, 82.765, 119.898
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
11A-405-

HOH

21B-408-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A34 - 195
2010B34 - 195

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Components

#1: Protein Protein tyrosine phosphatase TpbA


Mass: 24007.463 Da / Num. of mol.: 2
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 1.7M ammonium phosphate monobasic, 0.1M Tris, 7%(v/v) PEG400, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 25665 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.03→2.12 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→35.99 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 17.908 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25037 1688 7.8 %RANDOM
Rwork0.21995 ---
obs0.22236 19907 82.44 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.505 Å2
Baniso -1Baniso -2Baniso -3
1-10.61 Å20 Å2-0 Å2
2---5.22 Å20 Å2
3----5.38 Å2
Refinement stepCycle: LAST / Resolution: 2.03→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 16 25 2547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192565
X-RAY DIFFRACTIONr_bond_other_d0.0020.022453
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9553478
X-RAY DIFFRACTIONr_angle_other_deg0.90935597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9735321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32923.333126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33315422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8271528
X-RAY DIFFRACTIONr_chiral_restr0.0710.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212955
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02609
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_it3.6473.9221290
X-RAY DIFFRACTIONr_mcbond_other3.6393.9211289
X-RAY DIFFRACTIONr_mcangle_it4.895.8741609
X-RAY DIFFRACTIONr_mcangle_other4.8925.8761610
X-RAY DIFFRACTIONr_scbond_it4.034.3321275
X-RAY DIFFRACTIONr_scbond_other3.9224.3081267
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6576.311858
X-RAY DIFFRACTIONr_long_range_B_refined8.00231.4682878
X-RAY DIFFRACTIONr_long_range_B_other8.01431.4532877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9635 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.028→2.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 85 -
Rwork0.373 1049 -
obs--59.72 %
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)
13.07780.04410.59533.02210.49362.56470.13-0.4619-0.36490.5553-0.06430.16530.1124-0.0992-0.06570.1094-0.04110.04050.1870.06720.516-55.7010.705-17.048
22.35480.2003-0.51893.3370.26024.6143-0.0072-0.22140.04980.41690.1344-0.33530.00670.2632-0.12720.0570.0283-0.06050.1277-0.02390.143-19.5354.094-17.612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 195
2X-RAY DIFFRACTION2B34 - 194

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