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- PDB-1evh: EVH1 DOMAIN FROM MURINE ENABLED IN COMPLEX WITH ACTA PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1evh
TitleEVH1 DOMAIN FROM MURINE ENABLED IN COMPLEX WITH ACTA PEPTIDE
Components
  • PROTEIN (MENA EVH1 DOMAIN)
  • Peptide ACTA
KeywordsCONTRACTILE PROTEIN / MOLECULAR RECOGNITION / ACTIN DYNAMICS
Function / homology
Function and homology information


Signaling by ROBO receptors / actin polymerization-dependent cell motility / profilin binding / actin polymerization or depolymerization / stress fiber / filopodium / cellular response to leukemia inhibitory factor / neural tube closure / actin filament organization / axon guidance ...Signaling by ROBO receptors / actin polymerization-dependent cell motility / profilin binding / actin polymerization or depolymerization / stress fiber / filopodium / cellular response to leukemia inhibitory factor / neural tube closure / actin filament organization / axon guidance / SH3 domain binding / actin cytoskeleton / lamellipodium / actin binding / actin cytoskeleton organization / neuron projection / focal adhesion / synapse / cytosol
Similarity search - Function
VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Protein enabled homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsPrehoda, K.E. / Lee, D.J. / Lim, W.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structure of the enabled/VASP homology 1 domain-peptide complex: a key component in the spatial control of actin assembly.
Authors: Prehoda, K.E. / Lee, D.J. / Lim, W.A.
History
DepositionApr 21, 1999Deposition site: BNL / Processing site: NDB
Revision 1.0May 21, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
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_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: PROTEIN (MENA EVH1 DOMAIN)
B: Peptide ACTA


Theoretical massNumber of molelcules
Total (without water)13,2792
Polymers13,2792
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-7 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.614, 62.566, 94.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein PROTEIN (MENA EVH1 DOMAIN) / WH1 DOMAIN


Mass: 12598.247 Da / Num. of mol.: 1 / Fragment: MENA 1-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: BRAIN / Plasmid: PBH4 / Species (production host): Escherichia coli / Gene (production host): MENA 1-112 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03173
#2: Protein/peptide Peptide ACTA


Mass: 680.790 Da / Num. of mol.: 1 / Fragment: PROLINE RICH REPEAT / Source method: obtained synthetically / Details: sequence from LISTERIA MONOCYTOGENES
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.87 Å3/Da / Density % sol: 34.1 %
Crystal growpH: 7.5
Details: 0.1 M NA HEPES, 70% SATURATED AMMONIUM PHOSPHATE, pH 7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlSeMet Mrna 1-1121drop
26 mMAC-FPPPPT-CONH21drop
360 %satammonium phosphate1reservoir
40.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.96859, 0.99984
DetectorType: ADSC / Detector: CCD / Date: Nov 15, 1998
RadiationMonochromator: SI FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.968591
20.999841
ReflectionResolution: 1.8→30 Å / Num. obs: 17747 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 9 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.83 Å / Rsym value: 22 / % possible all: 97.6
Reflection
*PLUS
% possible obs: 99.1 % / Num. measured all: 88290 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 91.4 % / Rmerge(I) obs: 0.358

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 975 10.2 %RANDOM
Rwork0.23 ---
all-9529 --
obs-9529 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.47 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.53 Å20 Å20 Å2
2--11.22 Å20 Å2
3----4.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 0 27 947
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 172 11.3 %
Rwork0.27 1347 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.229 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Rfactor Rfree: 0.286 / % reflection Rfree: 11.3 % / Rfactor Rwork: 0.27

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