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- PDB-1uru: Amphiphysin BAR domain from Drosophila -

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Basic information

Entry
Database: PDB / ID: 1uru
TitleAmphiphysin BAR domain from Drosophila
ComponentsAMPHIPHYSIN
KeywordsENDOCYTOSIS / COILED-COIL / MEMBRANE CURVATURE
Function / homology
Function and homology information


rhabdomere membrane biogenesis / organelle / rhabdomere development / Clathrin-mediated endocytosis / Neutrophil degranulation / regulation of muscle contraction / exocytosis / cleavage furrow / phospholipid binding / protein localization ...rhabdomere membrane biogenesis / organelle / rhabdomere development / Clathrin-mediated endocytosis / Neutrophil degranulation / regulation of muscle contraction / exocytosis / cleavage furrow / phospholipid binding / protein localization / synapse / plasma membrane / cytoplasm
Similarity search - Function
Amphiphysin / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 domain / Src homology 3 domains ...Amphiphysin / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å
AuthorsEvans, P.R. / Kent, H.M.
CitationJournal: Science / Year: 2004
Title: Bar Domains as Sensors of Membrane Curvature: The Amphiphysin Bar Structure
Authors: Peter, B.J. / Kent, H.M. / Mills, I.G. / Vallis, Y. / Butler, J.G. / Evans, P.R. / Mcmahon, H.T.
History
DepositionNov 6, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_struct_special_symmetry / reflns_shell / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMPHIPHYSIN


Theoretical massNumber of molelcules
Total (without water)28,2691
Polymers28,2691
Non-polymers00
Water66737
1
A: AMPHIPHYSIN

A: AMPHIPHYSIN


Theoretical massNumber of molelcules
Total (without water)56,5382
Polymers56,5382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)49.586, 49.586, 190.319
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2008-

HOH

21A-2017-

HOH

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Components

#1: Protein AMPHIPHYSIN /


Mass: 28269.152 Da / Num. of mol.: 1 / Fragment: BAR DOMAIN, RESIDUES 1-244
Source method: isolated from a genetically manipulated source
Details: SEMET SUBSTITUTED / Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Description: GROWN IN MINIMAL MEDIUM + SEMET / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y092, UniProt: Q7KLE5*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.39 Å3/Da / Density % sol: 51.1 %
Crystal growMethod: vapor diffusion / pH: 6
Details: 2.5MG/ML PROTEIN SOLUTION IN 18% PEG4000, 200MM NACL, 1MM DTT, 20MM HEPES PH 7.4 MIXED WITH THE WELL SOLUTION 18% PEG 4000, 0.2M AMMONIUM ACETATE, 100MM SODIUM CITRATE PH 6.0. CRYSTALS WERE ...Details: 2.5MG/ML PROTEIN SOLUTION IN 18% PEG4000, 200MM NACL, 1MM DTT, 20MM HEPES PH 7.4 MIXED WITH THE WELL SOLUTION 18% PEG 4000, 0.2M AMMONIUM ACETATE, 100MM SODIUM CITRATE PH 6.0. CRYSTALS WERE EQUILIBRATED IN 20% GLYCEROL FOR COOLING TO 100K.
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mg/mlprotein1drop
218 %PEG40001drop
3200 mM1dropNaCl
41 mMdithiothreitol1drop
520 mMHEPES1drop
618 %PEG40001reservoir
70.2 Mammonium acetate1reservoir
8100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→31.94 Å / Num. obs: 8657 / % possible obs: 97.2 % / Redundancy: 10.21 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 4.9102
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 9.29 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 0.73 / % possible all: 86
Reflection shell
*PLUS
% possible obs: 86 % / Rmerge(I) obs: 0.01005 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.6→63.25 Å / SU B: 13.987 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 1.164 / ESU R Free: 0.402
RfactorNum. reflection% reflectionSelection details
Rfree0.30636 867 10 %RANDOM
Rwork0.23649 ---
obs0.23405 7786 97.21 %-
Displacement parametersBiso mean: 55.997 Å2
Baniso -1Baniso -2Baniso -3
1-3.03 Å21.52 Å20 Å2
2--3.03 Å20 Å2
3----4.55 Å2
Refinement stepCycle: LAST / Resolution: 2.6→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 0 37 1808
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.23405 / Rfactor obs: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.013

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