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- PDB-2i6p: Crystal structure of the complex of the archaeal sulfolobus PTP-f... -

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Basic information

Entry
Database: PDB / ID: 2i6p
TitleCrystal structure of the complex of the archaeal sulfolobus PTP-fold phosphatase with pNPP
ComponentsSulfolobus solfataricus protein tyrosine phosphatase
KeywordsHYDROLASE / PTP domain / tyrosine phosphatase
Function / homology
Function and homology information


dephosphorylation / protein tyrosine phosphatase activity / cytoplasm
Similarity search - Function
Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / 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. ...Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
4-NITROPHENYL PHOSPHATE / Protein phosphatase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfolobus solfataricus protein tyrosine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6362
Polymers18,4171
Non-polymers2191
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.200, 57.652, 42.517
Angle α, β, γ (deg.)90.00, 92.87, 90.00
Int Tables number4
Space group name H-MP1211

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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: Chemical ChemComp-4NP / 4-NITROPHENYL PHOSPHATE / Para-Nitrophenylphosphate


Mass: 219.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 5786 / Num. obs: 4664 / % possible obs: 80.6 % / Observed criterion σ(F): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.077 / Rsym value: 0.062 / Net I/σ(I): 17.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.77 / Num. unique all: 517 / Rsym value: 0.279 / % possible all: 91.7

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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: 2.5→30 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.284 --
Rwork0.224 --
all-5786 -
obs-4664 80.6 %
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 14 32 1329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3447
X-RAY DIFFRACTIONc_bond_d0.0072

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