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- PDB-2g6f: Crystal Structure of the SH3 Domain of betaPIX in Complex with a ... -

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Basic information

Entry
Database: PDB / ID: 2g6f
TitleCrystal Structure of the SH3 Domain of betaPIX in Complex with a High Affinity Peptide from PAK2
ComponentsRho guanine nucleotide exchange factor 7
KeywordsSIGNALING PROTEIN / SH3 domain / Peptide Interaction
Function / homology
Function and homology information


presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle ...presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle / RHOA GTPase cycle / storage vacuole / astrocyte cell migration / positive regulation of growth hormone secretion / postsynaptic actin cytoskeleton organization / gamma-tubulin binding / lamellipodium assembly / small GTPase-mediated signal transduction / mitotic spindle pole / Golgi organization / Rho protein signal transduction / GABA-ergic synapse / hematopoietic progenitor cell differentiation / ruffle / guanyl-nucleotide exchange factor activity / lamellipodium / cell cortex / growth cone / postsynapse / neuron projection / positive regulation of apoptotic process / focal adhesion / centrosome / neuronal cell body / protein kinase binding / protein-containing complex / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain ...Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
COBALT HEXAMMINE(III) / Rho guanine nucleotide exchange factor 7
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.92 Å
AuthorsHoelz, A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of the SH3 Domain of betaPIX in Complex with a High Affinity Peptide from PAK2
Authors: Hoelz, A. / Janz, J.M. / Lawrie, S.D. / Corwin, B. / Lee, A. / Sakmar, T.P.
History
DepositionFeb 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
X: Rho guanine nucleotide exchange factor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8922
Polymers6,7311
Non-polymers1611
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.377, 31.427, 28.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11X-213-

HOH

21X-266-

HOH

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Components

#1: Protein Rho guanine nucleotide exchange factor 7 / PAK-interacting exchange factor beta / Beta-Pix


Mass: 6731.333 Da / Num. of mol.: 1 / Fragment: SH3 domain(residues 10-63)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgef7, Pak3bp, Pixb / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O55043
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M HEPES, 53% MPD, 200mM [Co(NH3)]Cl3, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979191 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 0.92→30 Å / Num. all: 46091 / Num. obs: 46091 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 0.92 Å / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 0.92→28.17 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.547 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19896 2160 5 %RANDOM
Rwork0.18419 ---
all0.185 46091 --
obs0.18493 40642 92.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.797 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 0.92→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 25 309 1256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021498
X-RAY DIFFRACTIONr_bond_other_d0.0010.02422
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.914682
X-RAY DIFFRACTIONr_angle_other_deg0.6623975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90623.57128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.6031574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.32154
X-RAY DIFFRACTIONr_chiral_restr0.0630.265
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02115
X-RAY DIFFRACTIONr_nbd_refined0.1690.276
X-RAY DIFFRACTIONr_nbd_other0.1770.2421
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2232
X-RAY DIFFRACTIONr_nbtor_other0.0810.2281
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.226
X-RAY DIFFRACTIONr_mcbond_it1.1911.5379
X-RAY DIFFRACTIONr_mcbond_other0.4881.5126
X-RAY DIFFRACTIONr_mcangle_it1.4412464
X-RAY DIFFRACTIONr_scbond_it1.7893298
X-RAY DIFFRACTIONr_scangle_it1.9394.5215
X-RAY DIFFRACTIONr_rigid_bond_restr1.44331271
X-RAY DIFFRACTIONr_sphericity_free2.4543103
X-RAY DIFFRACTIONr_sphericity_bonded3.4133907
LS refinement shellResolution: 0.92→0.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 154 -
Rwork0.384 2757 -
obs--87.08 %

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