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- PDB-1f7c: CRYSTAL STRUCTURE OF THE BH DOMAIN FROM GRAF, THE GTPASE REGULATO... -

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Basic information

Entry
Database: PDB / ID: 1f7c
TitleCRYSTAL STRUCTURE OF THE BH DOMAIN FROM GRAF, THE GTPASE REGULATOR ASSOCIATED WITH FOCAL ADHESION KINASE
ComponentsRHOGAP PROTEIN
KeywordsSIGNALING PROTEIN / GAP / GTPase activating protein / Rho GTPase regulator / BH domain
Function / homology
Function and homology information


RHOA GTPase cycle / RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / RAC2 GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle / RHOQ GTPase cycle / RHOD GTPase cycle ...RHOA GTPase cycle / RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / RAC2 GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle / RHOQ GTPase cycle / RHOD GTPase cycle / mitophagy / GTPase activator activity / phospholipid binding / protein-macromolecule adaptor activity / cytoskeleton / endosome membrane / focal adhesion / signal transduction / mitochondrion / cytosol
Similarity search - Function
GRAF, SH3 domain / GRAF, BAR domain / : / : / BAR domain of APPL family / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / BAR domain / AH/BAR domain superfamily / Rho GTPase-activating protein domain ...GRAF, SH3 domain / GRAF, BAR domain / : / : / BAR domain of APPL family / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / BAR domain / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Variant SH3 domain / Rho GTPase activation protein / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho GTPase-activating protein 26 / Rho GTPase-activating protein 26
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MIR, molecular replacement / Resolution: 2.4 Å
AuthorsLongenecker, K.L. / Derewenda, U. / Sheffield, P.J. / Zheng, Y. / Derewenda, Z.S.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Structure of the BH domain from graf and its implications for Rho GTPase recognition.
Authors: Longenecker, K.L. / Zhang, B. / Derewenda, U. / Sheffield, P.J. / Dauter, Z. / Parsons, J.T. / Zheng, Y. / Derewenda, Z.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Expression, purification and crystallization of a BH domain from the GTPase regulatory protein associated with focal adhesion kinase
Authors: Sheffield, P.J. / Derewenda, U. / Taylor, J. / Parsons, T.J. / Derewenda, Z.S.
History
DepositionJun 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 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

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Assembly

Deposited unit
A: RHOGAP PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,4111
Polymers26,4111
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.026, 65.026, 91.624
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

21A-432-

HOH

Detailsmonomer provides biological activity

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Components

#1: Protein RHOGAP PROTEIN


Mass: 26411.467 Da / Num. of mol.: 1
Fragment: GTPASE ACTIVATING PROTEIN (GAP) FOR RHO FAMILY GTPASES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q98935, UniProt: Q5ZMW5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: PEG 6000, Na HEPES, pH 7.0, VAPOR DIFFUSION, temperature 294K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
220-22 %PEG60001reservoir
3100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 30884 / Num. obs: 9063 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.326 / Num. unique all: 866 / % possible all: 97.5
Reflection
*PLUS
Num. obs: 9020 / Num. measured all: 30884
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
AMoREphasing
MLPHAREphasing
CNS0.9refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR, molecular replacement / Resolution: 2.4→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 879 9 %Random
Rwork0.205 ---
all-9147 --
obs-9063 99.1 %-
Solvent computationSolvent model: CNS 0.9 / Bsol: 42.5 Å2
Displacement parametersBiso mean: 47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 0 47 1483
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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