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- PDB-2dxp: Crystal structure of the complex of the archaeal sulfolobus PTP-f... -

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Basic information

Entry
Database: PDB / ID: 2dxp
TitleCrystal structure of the complex of the archaeal sulfolobus PTP-fold phosphatase with phosphopeptides A-(p)Y-R
Components
  • A(PTR)R
  • Sulfolobus solfataricus protein tyrosine phosphatase
KeywordsHYDROLASE / PTP domain
Function / homology
Function and homology information


protein tyrosine phosphatase activity / cytoplasm
Similarity search - Function
: / Polymorphic toxin system, DSP-PTPase phosphatase / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / PTP type protein phosphatase domain profile. / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...: / Polymorphic toxin system, DSP-PTPase phosphatase / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / PTP type protein phosphatase domain profile. / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChu, H.M. / Wang, A.H.J.
CitationJournal: Proteins / Year: 2006
Title: Enzyme-substrate interactions revealed by the crystal structures of the archaeal Sulfolobus PTP-fold phosphatase and its phosphopeptide complexes
Authors: Chu, H.M. / Wang, A.H.J.
History
DepositionAug 29, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfolobus solfataricus protein tyrosine phosphatase
B: A(PTR)R


Theoretical massNumber of molelcules
Total (without water)18,9072
Polymers18,9072
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-5 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.539, 58.232, 36.475
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-5288-

HOH

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Components

#1: Protein Sulfolobus solfataricus protein tyrosine phosphatase / SsoPTP


Mass: 18417.100 Da / Num. of mol.: 1 / Mutation: C96S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q97VZ7, protein-tyrosine-phosphatase
#2: Protein/peptide A(PTR)R


Mass: 489.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.99→100 Å / Num. all: 10656 / Num. obs: 9678 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.083 / Rsym value: 0.055 / Net I/σ(I): 15.3
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 1.67 / Rsym value: 0.578

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Processing

Software
NameVersionClassification
CrystalClear(MSC/RIGAKU)data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OHE

1ohe


Resolution: 2.1→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.252 --
Rwork0.211 --
all-10656 -
obs-9678 90.8 %
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 0 88 1398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3042
X-RAY DIFFRACTIONc_bond_d0.00617

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