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- PDB-1wer: RAS-GTPASE-ACTIVATING DOMAIN OF HUMAN P120GAP -

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Basic information

Entry
Database: PDB / ID: 1wer
TitleRAS-GTPASE-ACTIVATING DOMAIN OF HUMAN P120GAP
ComponentsP120GAP
KeywordsGTPASE ACTIVATION / RAS / GAP / SIGNAL TRANSDUCTION / GROWTH REGULATION / CANCER
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 / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / 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. ...Ras GTPase-activating protein 1, N-terminal SH2 domain / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / 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 / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / 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 / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ras GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsScheffzek, K. / Lautwein, A. / Kabsch, W. / Ahmadian, M.R. / Wittinghofer, A.
Citation
Journal: Nature / Year: 1996
Title: Crystal structure of the GTPase-activating domain of human p120GAP and implications for the interaction with Ras.
Authors: Scheffzek, K. / Lautwein, A. / Kabsch, W. / Ahmadian, M.R. / Wittinghofer, A.
#1: Journal: Proteins / Year: 1997
Title: Crystallization and Preliminary X-Ray Crystallographic Study of the Ras-Gtpase-Activating Domain of Human P120Gap
Authors: Scheffzek, K. / Lautwein, A. / Scherer, A. / Franken, S. / Wittinghofer, A.
#2: Journal: Science / Year: 1988
Title: Molecular Cloning of Two Types of Gap Complementary DNA from Human Placenta
Authors: Trahey, M. / Wong, G. / Halenbeck, R. / Rubinfeld, B. / Martin, G.A. / Ladner, M. / Long, C.M. / Crosier, W.J. / Watt, K. / Koths, K. / Mccormick, F.
#3: Journal: Science / Year: 1987
Title: A Cytoplasmic Protein Stimulates Normal N-Ras P21 Gtpase, But Does not Affect Oncogenic Mutants
Authors: Trahey, M. / Mccormick, F.
History
DepositionNov 20, 1996Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P120GAP


Theoretical massNumber of molelcules
Total (without water)38,2231
Polymers38,2231
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.200, 55.600, 142.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein P120GAP / GAP-334 / GAPETTE


Mass: 38223.277 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 714 - 1047
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOSOL / Gene: GENE FRAGMENT OF P120GAP / Organ: PLACENTA / Plasmid: PTRCGAP-334
Gene (production host): GENE FRAGMENT OF P120GAP (POSITION 2258-3259)
Production host: Escherichia coli (E. coli) / Strain (production host): DG103 / References: UniProt: P20936
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.2 Å3/Da / Density % sol: 40 %
Crystal growpH: 6.5 / Details: SEE REFERENCE 1, pH 6.5
Crystal grow
*PLUS
Method: micro-seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
27-8.5 %PEG33501drop
350 mMMES1drop
4100 mM1dropMgCl2
5100 mMMES1reservoir
614-17 %PEG33501reservoir
7200 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 26, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 42457 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 15.4
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.2 / % possible all: 97
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 714 - 717 (N-TERMINUS) AND 1042 - 1047 (C-TERMINUS) ARE NOT VISIBLE IN THE ELECTRON DENSITY AND WERE NOT INCLUDED IN THE MODEL. RESIDUES 836 - 839 AND 982 - 988 SHOW WEAK ELECTRON ...Details: RESIDUES 714 - 717 (N-TERMINUS) AND 1042 - 1047 (C-TERMINUS) ARE NOT VISIBLE IN THE ELECTRON DENSITY AND WERE NOT INCLUDED IN THE MODEL. RESIDUES 836 - 839 AND 982 - 988 SHOW WEAK ELECTRON DENSITY FOR MAIN- AND SIDE-CHAIN ATOMS AND WERE MODELLED STEREOCHEMICALLY. THE SIDE CHAINS OF THE FOLLOWING RESIDUES SHOW WEAK OR PARTIAL ELECTRON DENSITY: GLU 720, GLU 721, GLU 722, LYS 733, GLU 734, GLN 747, GLU 783, ARG 789, LYS 803, LYS 820, LYS 826, GLN 827, LYS 858, ARG 894, LYS 949, GLU 950, TYR 952, LYS 961, THR 989, ASP 990, ARG 993, ASP 994, GLU 1000, ASP 1007, GLU 1015, ARG 1016, LYS 1024, LYS 1025, ASN 1038.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 4074 10 %RANDOM
Rwork0.221 ---
obs0.221 40803 97.9 %-
Displacement parametersBiso mean: 26.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 0 181 2952
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.56
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.551.5
X-RAY DIFFRACTIONx_mcangle_it2.442
X-RAY DIFFRACTIONx_scbond_it2.992
X-RAY DIFFRACTIONx_scangle_it4.742.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 696 10.5 %
Rwork0.301 5917 -
obs--96.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.56
LS refinement shell
*PLUS
Rfactor obs: 0.301

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