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- PDB-1pbv: SEC7 DOMAIN OF THE EXCHANGE FACTOR ARNO -

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Basic information

Entry
Database: PDB / ID: 1pbv
TitleSEC7 DOMAIN OF THE EXCHANGE FACTOR ARNO
ComponentsARNO
KeywordsEXCHANGE FACTOR / SEC7 / ARNO / ARF FUNCTIONAL CLASS: GUANINE NUCLEOTIDE EXCHANGE FACTOR
Function / homology
Function and homology information


Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / guanyl-nucleotide exchange factor activity / adherens junction / endocytosis / growth cone / actin cytoskeleton organization / Golgi membrane ...Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / guanyl-nucleotide exchange factor activity / adherens junction / endocytosis / growth cone / actin cytoskeleton organization / Golgi membrane / lipid binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 ...Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsCherfils, J. / Menetrey, J. / Mathieu, M. / Le Bras, G. / Robineau, S. / Beraud-Dufour, S. / Antonny, B. / Chardin, P.
CitationJournal: Nature / Year: 1998
Title: Structure of the Sec7 domain of the Arf exchange factor ARNO.
Authors: Cherfils, J. / Menetrey, J. / Mathieu, M. / Le Bras, G. / Robineau, S. / Beraud-Dufour, S. / Antonny, B. / Chardin, P.
History
DepositionJan 15, 1998Processing site: BNL
Revision 1.0Mar 9, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 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: ARNO


Theoretical massNumber of molelcules
Total (without water)22,4571
Polymers22,4571
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.766, 89.766, 89.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein ARNO / ARF NUCLEOTIDE-BINDING SITE OPENER


Mass: 22456.744 Da / Num. of mol.: 1 / Fragment: SEC7 DOMAIN, RESIDUES 50 - 252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q99418
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.87 Å3/Da / Density % sol: 50 % / Description: HEAVY ATOM DERIVATIVES EMTS AND K2HGI4
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
212.5 %PEG40001reservoir
3200 mM1reservoirLiSO4
43.5 %propanol1reservoir
51 mMdithiothreitol1reservoir
6100 mMEPPS1reservoir

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteTypeIDWavelength
SYNCHROTRONLURE LURE BEAMLINE10.97
SYNCHROTRONESRF ESRF 21.0079
Detector
TypeID
MARRESEARCH1
CCD CAMERA2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.00791
ReflectionResolution: 2→15 Å / Num. obs: 70772 / % possible obs: 97.6 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 4.2
Reflection
*PLUS
Num. obs: 16226 / Num. measured all: 70772 / Rmerge(I) obs: 0.042

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.84model building
X-PLOR3.84refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.84phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2→15 Å /
Rfactor% reflection
Rfree0.226 10 %
Rwork0.182 -
obs0.182 -
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 0 138 1718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.049
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.7 Å2

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