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- PDB-2i6j: Crystal structure of the complex of the archaeal sulfolobus PTP-f... -

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Basic information

Entry
Database: PDB / ID: 2i6j
TitleCrystal structure of the complex of the archaeal sulfolobus PTP-fold phosphatase with phosphate ion
ComponentsSulfolobus 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. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...: / 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. / Protein-tyrosine phosphatase / 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
PHOSPHATE ION / Protein phosphatase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Sulfolobus solfataricus protein tyrosine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5282
Polymers18,4331
Non-polymers951
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.289, 72.289, 32.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Sulfolobus solfataricus protein tyrosine phosphatase / SsoPTP


Mass: 18433.164 Da / Num. of mol.: 1
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 22463 / Num. obs: 19596 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.46 / Rsym value: 0.4 / Net I/σ(I): 25.1
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.26 / Num. unique all: 1640 / Rsym value: 0.41

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OHE

1ohe


Resolution: 1.66→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.241 --
Rwork0.208 --
all-22463 -
obs-19596 87.2 %
Refinement stepCycle: LAST / Resolution: 1.66→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 5 142 1445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.443

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