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- PDB-1usd: human VASP tetramerisation domain L352M -

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Basic information

Entry
Database: PDB / ID: 1usd
Titlehuman VASP tetramerisation domain L352M
ComponentsVASODILATOR-STIMULATED PHOSPHOPROTEIN
KeywordsSIGNALING PROTEIN / PHOSPHORYLATION / ACTIN-BINDING / KINASE
Function / homology
Function and homology information


profilin binding / Signaling by ROBO receptors / Cell-extracellular matrix interactions / actin polymerization or depolymerization / filopodium membrane / positive regulation of actin filament polymerization / lamellipodium membrane / Generation of second messenger molecules / bicellular tight junction / neural tube closure ...profilin binding / Signaling by ROBO receptors / Cell-extracellular matrix interactions / actin polymerization or depolymerization / filopodium membrane / positive regulation of actin filament polymerization / lamellipodium membrane / Generation of second messenger molecules / bicellular tight junction / neural tube closure / axon guidance / SH3 domain binding / actin cytoskeleton / actin binding / actin cytoskeleton organization / protein homotetramerization / cadherin binding / focal adhesion / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Vasodilator-stimulated phosphoprotein / Vasodilator-stimulated phosphoprotein/ENA/VASP-like / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Vasodilator-stimulated phosphoprotein / Vasodilator-stimulated phosphoprotein/ENA/VASP-like / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vasodilator-stimulated phosphoprotein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKuhnel, K. / Jarchau, T. / Wolf, E. / Schlichting, I. / Walter, U. / Wittinghofer, A. / Strelkov, S.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The Vasp Tetramerization Domain is a Right-Handed Coiled Coil Based on a 15-Residue Repeat
Authors: Kuhnel, K. / Jarchau, T. / Wolf, E. / Schlichting, I. / Walter, U. / Wittinghofer, A. / Strelkov, S.V.
History
DepositionNov 21, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VASODILATOR-STIMULATED PHOSPHOPROTEIN


Theoretical massNumber of molelcules
Total (without water)5,3151
Polymers5,3151
Non-polymers00
Water81145
1
A: VASODILATOR-STIMULATED PHOSPHOPROTEIN

A: VASODILATOR-STIMULATED PHOSPHOPROTEIN

A: VASODILATOR-STIMULATED PHOSPHOPROTEIN

A: VASODILATOR-STIMULATED PHOSPHOPROTEIN


Theoretical massNumber of molelcules
Total (without water)21,2604
Polymers21,2604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665y+1,-x+1,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation2_755-x+2,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)29.648, 29.648, 100.444
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/peptide VASODILATOR-STIMULATED PHOSPHOPROTEIN / VASP


Mass: 5315.037 Da / Num. of mol.: 1 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 335-379 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P50552
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE LEU 351 MET, CHAIN A FUNCTION: ACTIN- AND PROFILIN-BINDING MICROFILAMENT- ...ENGINEERED RESIDUE LEU 351 MET, CHAIN A FUNCTION: ACTIN- AND PROFILIN-BINDING MICROFILAMENT-ASSOCIATED PROTEIN.

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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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growpH: 8.5
Details: 25% PEG MME550, 0.2M NA-CITRATE, 0.1M TRIS PH8.5, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorDate: May 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 54657 / % possible obs: 99.8 % / Redundancy: 3 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.035
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.309 / % possible all: 99.9

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→20 Å / SU B: 3.318 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.224 218 5 %RANDOM
Rwork0.211 ---
obs0.212 4773 99.9 %-
Displacement parametersBiso mean: 11 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2---1.17 Å20 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms338 0 0 45 383

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