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- PDB-4jxh: Complexe of ARNO Sec7 domain with the protein-protein interaction... -

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Basic information

Entry
Database: PDB / ID: 4jxh
TitleComplexe of ARNO Sec7 domain with the protein-protein interaction inhibitor N-(4-hydroxy-2,6-dimethylphenyl)benzenesulfonamide at pH 8.5
ComponentsCytohesin-2
KeywordsSIGNALING PROTEIN/INHIBITOR / sec 7 domain / NUCLEOTIDE EXCHANGE FACTOR / ARF1 / SIGNALING PROTEIN-INHIBITOR complex
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
Chem-HRC / PHOSPHATE ION / Cytohesin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 28, 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Cytohesin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2913
Polymers24,9181
Non-polymers3722
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.470, 89.470, 89.470
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: 24918.410 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: Chemical ChemComp-HRC / N-(4-hydroxy-2,6-dimethylphenyl)benzenesulfonamide


Mass: 277.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15NO3S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M MgSO4, 18% PEG 5000 MME, 0.1M TRIS- HCL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.47→36.55 Å / Num. all: 40862 / Num. obs: 38676 / % possible obs: 99.67 %
Reflection shellResolution: 1.469→1.508 Å / % possible all: 99.7

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JMI

4jmi


Resolution: 1.47→36.55 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.52 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16807 2044 5 %RANDOM
Rwork0.13357 ---
obs0.13531 38676 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.591 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.47→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1582 0 24 305 1911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191637
X-RAY DIFFRACTIONr_bond_other_d0.0020.021571
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9892207
X-RAY DIFFRACTIONr_angle_other_deg0.96333601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6585194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21124.30286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69315298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7421514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211859
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02398
X-RAY DIFFRACTIONr_rigid_bond_restr1.39833208
X-RAY DIFFRACTIONr_sphericity_free42.957576
X-RAY DIFFRACTIONr_sphericity_bonded12.01953407
LS refinement shellResolution: 1.469→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 135 -
Rwork0.139 2862 -
obs--100 %

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