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- PDB-1wvh: Crystal structure of tensin1 PTB domain -

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Basic information

Entry
Database: PDB / ID: 1wvh
TitleCrystal structure of tensin1 PTB domain
ComponentsTensin
KeywordsCELL ADHESION / beta sandwich
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / fibroblast migration / phosphoprotein phosphatase activity / actin binding / cytoskeleton / focal adhesion / cell surface / cytoplasm
Similarity search - Function
Tensin, phosphotyrosine-binding domain / Tensin-like, SH2 domain / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein ...Tensin, phosphotyrosine-binding domain / Tensin-like, SH2 domain / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / C2 domain superfamily / Protein-tyrosine phosphatase-like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsMcCleverty, C.J. / Liddington, R.C.
CitationJournal: Protein Sci. / Year: 2007
Title: Structure of the PTB domain of tensin1 and a model for its recruitment to fibrillar adhesions.
Authors: McCleverty, C.J. / Lin, D.C. / Liddington, R.C.
History
DepositionDec 15, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tensin


Theoretical massNumber of molelcules
Total (without water)14,6411
Polymers14,6411
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.680, 75.680, 48.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Tensin / / tensin1


Mass: 14640.666 Da / Num. of mol.: 1 / Fragment: PTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q04205
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.5 Å3/Da / Density % sol: 48.311153 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: PEG 600, CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979, 0.9793, 0.8731
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2003
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.87311
ReflectionResolution: 1.5→20 Å / Num. all: 22134 / Num. obs: 22134 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.5→1.59 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1050 5 %random
Rwork0.218 ---
obs0.218 21003 --
all-21003 --
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1016 0 0 104 1120
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.34 22 -
Rwork0.29 --
obs-3479 99.6 %

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