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- PDB-2j05: Crystal structure of the RasGAP SH3 domain at 1.5 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 2j05
TitleCrystal structure of the RasGAP SH3 domain at 1.5 Angstrom resolution
ComponentsRAS GTPASE-ACTIVATING PROTEIN 1
KeywordsSIGNAL TRANSDUCTION / GTPASE ACTIVATION / SH3 DOMAIN / SH2 DOMAIN / SRC HOMOLOGY 3 / RAS SIGNALING PATHWAY / GTPASE ACTIVATING PROTEIN / PROTO-ONCOGENE / PHOSPHORYLATION / DISEASE MUTATION
Function / homology
Function and homology information


regulation of RNA metabolic process / regulation of actin filament polymerization / potassium channel inhibitor activity / negative regulation of cell adhesion / blood vessel morphogenesis / negative regulation of cell-matrix adhesion / mitotic cytokinesis / ephrin receptor signaling pathway / vasculogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases ...regulation of RNA metabolic process / regulation of actin filament polymerization / potassium channel inhibitor activity / negative regulation of cell adhesion / blood vessel morphogenesis / negative regulation of cell-matrix adhesion / mitotic cytokinesis / ephrin receptor signaling pathway / vasculogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ruffle / EPHB-mediated forward signaling / phosphotyrosine residue binding / Downstream signal transduction / GTPase activator activity / VEGFR2 mediated cell proliferation / Regulation of RAS by GAPs / GTPase binding / regulation of cell shape / negative regulation of neuron apoptotic process / intracellular signal transduction / signaling receptor binding / GTPase activity / negative regulation of apoptotic process / signal transduction / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ras GTPase-activating protein 1, N-terminal SH2 domain / RasGAP, SH3 domain / Ras GTPase-activating protein 1, C-terminal SH2 domain / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain ...Ras GTPase-activating protein 1, N-terminal SH2 domain / RasGAP, SH3 domain / Ras GTPase-activating protein 1, C-terminal SH2 domain / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Rho GTPase activation protein / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / SH3 Domains / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Ras GTPase-activating protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsRoss, B. / Gajhede, M. / Kristensen, O.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: High Resolution Crystal Structures of the P120 Rasgap SH3 Domain.
Authors: Ross, B. / Kristensen, O. / Favre, D. / Walicki, J. / Kastrup, J.S. / Widmann, C. / Gajhede, M.
History
DepositionAug 1, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAS GTPASE-ACTIVATING PROTEIN 1
B: RAS GTPASE-ACTIVATING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)15,5312
Polymers15,5312
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.800, 32.800, 183.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.88766, 0.3578, 0.28989), (-0.45063, -0.80452, -0.38689), (0.09479, -0.47406, 0.87538)
Vector: 3.32015, 61.96505, 30.50249)

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Components

#1: Protein RAS GTPASE-ACTIVATING PROTEIN 1 / GTPASE-ACTIVATING PROTEIN / GAP / RAS P21 PROTEIN ACTIVATOR / P120GAP / RASGAP


Mass: 7765.334 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 281-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20936
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growpH: 9 / Details: 100 MM KNO3, 100 MM TAPS, PH 9 AND 40% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: May 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→45 Å / Num. obs: 35348 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 7.3 / % possible all: 89.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→28.41 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 918214.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1750 5 %RANDOM
Rwork0.177 ---
obs0.177 34709 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.876 Å2 / ksol: 0.393641 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.82 Å20 Å2
2--0.48 Å20 Å2
3----0.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.5→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 0 117 1140
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.771.5
X-RAY DIFFRACTIONc_mcangle_it2.692
X-RAY DIFFRACTIONc_scbond_it32
X-RAY DIFFRACTIONc_scangle_it4.632.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 283 5.4 %
Rwork0.246 4931 -
obs--90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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