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- PDB-2w6b: Crystal Structure of the Trimeric beta-PIX Coiled-Coil Domain -

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Basic information

Entry
Database: PDB / ID: 2w6b
TitleCrystal Structure of the Trimeric beta-PIX Coiled-Coil Domain
ComponentsRHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7
KeywordsSIGNALING PROTEIN / PHOSPHOPROTEIN / GUANINE-NUCLEOTIDE RELEASING FACTOR / GIT / PAK / PIX / COOL / RAC1 / GIT1 / CDC42 / COOL-1 / ARHGEF7 / BETA-PIX / SH3 DOMAIN / COILED-COIL
Function / homology
Function and homology information


negative regulation of microtubule nucleation / presynaptic actin cytoskeleton organization / Ephrin signaling / NRAGE signals death through JNK / EGFR downregulation / RHOU GTPase cycle / RHOV GTPase cycle / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle ...negative regulation of microtubule nucleation / presynaptic actin cytoskeleton organization / Ephrin signaling / NRAGE signals death through JNK / EGFR downregulation / RHOU GTPase cycle / RHOV GTPase cycle / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle / postsynaptic actin cytoskeleton organization / RHOA GTPase cycle / positive regulation of growth hormone secretion / storage vacuole / astrocyte cell migration / gamma-tubulin binding / lamellipodium assembly / small GTPase-mediated signal transduction / mitotic spindle pole / Golgi organization / Rho protein signal transduction / hematopoietic progenitor cell differentiation / ruffle / guanyl-nucleotide exchange factor activity / GABA-ergic synapse / lamellipodium / growth cone / cell cortex / postsynapse / neuron projection / positive regulation of apoptotic process / focal adhesion / neuronal cell body / centrosome / protein kinase binding / protein-containing complex / plasma membrane / cytosol / cytoplasm
Similarity search - Function
L1 transposable element, trimerization 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 ...L1 transposable element, trimerization 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. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 7
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSchlenker, O. / Rittinger, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structures of Dimeric Git1 and Trimeric Beta-Pix and Implications for Git-Pix Complex Assembly.
Authors: Schlenker, O. / Rittinger, K.
History
DepositionDec 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7


Theoretical massNumber of molelcules
Total (without water)6,6511
Polymers6,6511
Non-polymers00
Water27015
1
A: RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7

A: RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7

A: RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7


Theoretical massNumber of molelcules
Total (without water)19,9543
Polymers19,9543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation2_565-y,x-y+1,z1
Buried area5830 Å2
ΔGint-50.5 kcal/mol
Surface area11170 Å2
MethodPQS
Unit cell
Length a, b, c (Å)43.120, 43.120, 79.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7 / BETA-PIX / PAK-INTERACTING EXCHANGE FACTOR BETA / BETA-PIX


Mass: 6651.386 Da / Num. of mol.: 1 / Fragment: COILED-COIL, RESIDUES 588-638
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O55043
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CRYSTALLIZED PROTEIN INCLUDES ONLY THE COILED-COIL DOMAIN OF BETA-PIX AND AS A CLONING ARTIFACT ...THE CRYSTALLIZED PROTEIN INCLUDES ONLY THE COILED-COIL DOMAIN OF BETA-PIX AND AS A CLONING ARTIFACT THE N-TERMINAL RESIDUES GPLGS.

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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: 3.3 Å3/Da / Density % sol: 62 %
Description: RESIDUES 230 TO 278 OF CHAIN C OF PDB ID 2BA2 WERE USED FOR MR. SEQUENCE ASSIGNMENT WAS CONFIRMED USING ANOMALOUS DIFFERENCE MAPS TO VERIFY THE PRESENCE OF THE SELENIUM SITES.
Crystal growDetails: 35% MPD, 0.24 M NON-DETERGENT SULPHOBETAINE 195 (NDSB-195)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9698
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9698 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 2079 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 21 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 22 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 14.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BA2

2ba2


Resolution: 2.8→39.72 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / ESU R: 0.94 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BIOLOGICALLY RELEVANT MOLECULE IS ARRANGED AROUND A NON-CRYSTALLOGRAPHIC THREEFOLD AXIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.305 95 4.5 %RANDOM
Rwork0.278 ---
obs0.279 1993 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20.72 Å20 Å2
2--1.43 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms408 0 0 15 423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022408
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5632.009544
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09725.26319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.4011589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.484154
X-RAY DIFFRACTIONr_chiral_restr0.0920.265
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02288
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.2184
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2272
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.223
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.223
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_it0.4811.5259
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9882410
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5693149
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.824.5134
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 7
Rwork0.386 165

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