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- PDB-1i49: CRYSTAL STRUCTURE ANALYSIS OF ARFAPTIN -

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Basic information

Entry
Database: PDB / ID: 1i49
TitleCRYSTAL STRUCTURE ANALYSIS OF ARFAPTIN
ComponentsARFAPTIN 2
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


membrane curvature sensor activity / Retrograde transport at the Trans-Golgi-Network / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to phagophore assembly site / GTP-dependent protein binding / ruffle organization / phosphatidylinositol-4-phosphate binding / lamellipodium assembly / small GTPase-mediated signal transduction / mitophagy ...membrane curvature sensor activity / Retrograde transport at the Trans-Golgi-Network / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to phagophore assembly site / GTP-dependent protein binding / ruffle organization / phosphatidylinositol-4-phosphate binding / lamellipodium assembly / small GTPase-mediated signal transduction / mitophagy / ruffle / trans-Golgi network membrane / phospholipid binding / intracellular protein transport / small GTPase binding / cell cortex / actin cytoskeleton organization / cadherin binding / protein domain specific binding / GTP binding / nucleolus / Golgi apparatus / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / Arfaptin homology (AH) domain/BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsTarricone, C. / Xiao, B. / Justin, N. / Gamblin, S.J. / Smerdon, S.J.
CitationJournal: Nature / Year: 2001
Title: The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways.
Authors: Tarricone, C. / Xiao, B. / Justin, N. / Walker, P.A. / Rittinger, K. / Gamblin, S.J. / Smerdon, S.J.
History
DepositionFeb 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.4Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: ARFAPTIN 2
B: ARFAPTIN 2


Theoretical massNumber of molelcules
Total (without water)51,2282
Polymers51,2282
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-38 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.334, 146.334, 82.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ARFAPTIN 2 /


Mass: 25614.057 Da / Num. of mol.: 2 / Fragment: RESIDUES 118-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P53365
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 4.99 Å3/Da / Density % sol: 75.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: TRI-SODIUM CITRATE DIHYDRATE, ISOPROPANOL, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 Mtri-sodium citrate dihydrate1reservoir
310 %(v/v)isopropanol1reservoir
450 mMsodium HEPES1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX9.610.87
SYNCHROTRONESRF BM1420.9785
SYNCHROTRONESRF BM1430.979
SYNCHROTRONESRF BM1440.8856
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 30, 1999
ADSC QUANTUM 42CCDJun 3, 1999
ADSC QUANTUM 43CCDJun 3, 1999
ADSC QUANTUM 44CCDJun 3, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
20.97851
30.9791
40.88561
ReflectionResolution: 2.8→30 Å / Num. all: 25459 / Num. obs: 25169 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 28.9
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 3 % / Rmerge(I) obs: 0.309 / Num. unique all: 3134

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.275 1260 Random
Rwork0.234 --
all-25459 -
obs-25169 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 0 225 3442
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.008
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2

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