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- PDB-4jmi: Sec7 domain of ARNO, an exchange factor, at 1.5 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 4jmi
TitleSec7 domain of ARNO, an exchange factor, at 1.5 Angstrom resolution
ComponentsCytohesin-2
KeywordsSIGNALING PROTEIN / Nucleotide Exchange Factors / Arf1
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHoh, F. / Rouhana, J.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Fragment-based identification of a locus in the Sec7 domain of Arno for the design of protein-protein interaction inhibitors
Authors: Rouhana, J. / Hoh, F. / Estaran, S. / Henriquet, C. / Boublik, Y. / Kerkour, A. / Trouillard, R. / Martinez, J. / Pugniere, M. / Padilla, A. / Chavanieu, A.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Structure summary
Revision 1.3Apr 23, 2014Group: Database references
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytohesin-2


Theoretical massNumber of molelcules
Total (without water)23,0291
Polymers23,0291
Non-polymers00
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.540, 89.540, 89.540
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 Cytohesin-2 / ARF exchange factor / ARF nucleotide-binding site opener / Protein ARNO / PH / SEC7 and coiled-coil ...ARF exchange factor / ARF nucleotide-binding site opener / Protein ARNO / PH / SEC7 and coiled-coil domain-containing protein 2


Mass: 23029.312 Da / Num. of mol.: 1 / Fragment: Sec7 domain, UNP residues 56-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYTH2, ARNO, PSCD2, PSCD2L / Plasmid: pET28-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99418
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M MgSO4, Peg 5000 MME 18%, 0.1M Mes pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97628 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.5→44.77 Å / Num. all: 38574 / Num. obs: 38574 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.342 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBV

1pbv


Resolution: 1.5→44.77 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.661 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16616 1927 5 %RANDOM
Rwork0.13287 ---
obs0.13459 36594 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.079 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 0 291 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191580
X-RAY DIFFRACTIONr_bond_other_d0.0010.021533
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.9712125
X-RAY DIFFRACTIONr_angle_other_deg0.74733515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7625191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61824.09683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.215292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1821514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02383
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3581.695767
X-RAY DIFFRACTIONr_mcbond_other1.3591.691766
X-RAY DIFFRACTIONr_mcangle_it1.6772.547957
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2082.111813
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.73533113
X-RAY DIFFRACTIONr_sphericity_free27.881566
X-RAY DIFFRACTIONr_sphericity_bonded8.09153309
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 120 -
Rwork0.11 2692 -
obs--100 %

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