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- PDB-2m3v: Solution structure of tyrosine phosphatase related to biofilm for... -

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Basic information

Entry
Database: PDB / ID: 2m3v
TitleSolution structure of tyrosine phosphatase related to biofilm formation A (TpbA) from Pseudomonas aeruginosa
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / Dual Specificity Phosphatase
Function / homology
Function and homology information


protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / 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
Dual specificity protein phosphatase TpbA / Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKoveal, D. / Peti, W. / Page, R.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Ligand Binding Reduces Conformational Flexibility in the Active Site of Tyrosine Phosphatase Related to Biofilm Formation A (TpbA) from Pseudomonasaeruginosa.
Authors: Koveal, D. / Clarkson, M.W. / Wood, T.K. / Page, R. / Peti, W.
History
DepositionJan 26, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)21,3681
Polymers21,3681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative uncharacterized protein


Mass: 21368.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: PA14_13660 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02S50, UniProt: A0A0H2ZFK2*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
1323D C(CO)NH
1423D HNCA
1523D HN(CA)CB
1623D HBHA(CO)NH
1713D 1H-15N NOESY
1832D 1H-1H TOCSY
1932D 1H-1H NOESY
11023D (H)CCH-TOCSY
11123D (H)CCH-COSY
11223D (H)CCH-TOCSY
11323D 1H-13C NOESY
11412D 1H-15N HSQC
11523D HN(CA)CB
11643D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-99% 15N] TpbA, 10 mM TRIS, 100 mM sodium chloride, 0.5 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-99% 13C; U-99% 15N] TpbA, 10 mM TRIS, 100 mM sodium chloride, 0.5 mM TCEP-8, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM TpbA-9, 10 mM TRIS, 100 mM sodium chloride, 0.5 mM TCEP, 100% D2O100% D2O
41.0 mM [U-99% 13C; U-99% 15N; U-48% 2H] TpbA, 10 mM TRIS, 100 mM sodium chloride, 0.5 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMTpbA-1[U-99% 15N]1
10 mMTRIS-21
100 mMsodium chloride-31
0.5 mMTCEP-41
1.0 mMTpbA-5[U-99% 13C; U-99% 15N]2
10 mMTRIS-62
100 mMsodium chloride-72
0.5 mMTCEP-82
1.0 mMTpbA-93
10 mMTRIS-103
100 mMsodium chloride-113
0.5 mMTCEP-123
1.0 mMTpbA-13[U-99% 13C; U-99% 15N; U-48% 2H]4
10 mMTRIS-144
100 mMsodium chloride-154
0.5 mMTCEP-164
Sample conditionsIonic strength: 0.1 / pH: 7.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CYANA_2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS_1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOS+Cornilescu, Delaglio and Baxdihedral angle restraints
RefinementMethod: simulated annealing / Software ordinal: 1
Details: RECOORD scripts were used (Nederveen et al. Proteins. 2005.)
NMR constraintsNOE constraints total: 2504 / NOE intraresidue total count: 581 / NOE long range total count: 707 / NOE medium range total count: 515 / NOE sequential total count: 701 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 135 / Protein psi angle constraints total count: 135
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4.83 ° / Maximum upper distance constraint violation: 0.3 Å
NMR ensemble rmsDistance rms dev: 0.0175 Å / Distance rms dev error: 0.001 Å

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