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- PDB-3w6r: Crystal structure of the GAP domain of human MgcRacGAP -

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Basic information

Entry
Database: PDB / ID: 3w6r
TitleCrystal structure of the GAP domain of human MgcRacGAP
ComponentsRac GTPase-activating protein 1
KeywordsSIGNALING PROTEIN / GTPase activating
Function / homology
Function and homology information


centralspindlin complex / actomyosin contractile ring assembly / sulfate transport / mitotic spindle midzone assembly / regulation of attachment of spindle microtubules to kinetochore / gamma-tubulin binding / RHOD GTPase cycle / Flemming body / Kinesins / regulation of small GTPase mediated signal transduction ...centralspindlin complex / actomyosin contractile ring assembly / sulfate transport / mitotic spindle midzone assembly / regulation of attachment of spindle microtubules to kinetochore / gamma-tubulin binding / RHOD GTPase cycle / Flemming body / Kinesins / regulation of small GTPase mediated signal transduction / COPI-dependent Golgi-to-ER retrograde traffic / RHOB GTPase cycle / beta-tubulin binding / RHOC GTPase cycle / positive regulation of cytokinesis / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / regulation of embryonic development / CDC42 GTPase cycle / Rho protein signal transduction / mitotic cytokinesis / alpha-tubulin binding / RHOA GTPase cycle / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / monoatomic ion transport / RAC1 GTPase cycle / MHC class II antigen presentation / erythrocyte differentiation / GTPase activator activity / acrosomal vesicle / cytoplasmic side of plasma membrane / mitotic spindle / spindle / protein-macromolecule adaptor activity / midbody / spermatogenesis / microtubule binding / microtubule / protein kinase binding / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phorbol esters/diacylglycerol binding domain (C1 domain) / Rho GTPase activation protein / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. ...Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phorbol esters/diacylglycerol binding domain (C1 domain) / Rho GTPase activation protein / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rac GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMatsuura, A. / Lee, H.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Crystal structure of GTPase-activating domain from human MgcRacGAP.
Authors: Matsuura, A. / Lee, H.H.
History
DepositionFeb 21, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rac GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)22,7891
Polymers22,7891
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.466, 63.159, 74.078
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 Rac GTPase-activating protein 1 / Male germ cell RacGap / MgcRacGAP / Protein CYK4 homolg / CYK4 / HsCYK-4


Mass: 22788.615 Da / Num. of mol.: 1 / Fragment: Rho-GAP domain, UNP RESIDUES 348-546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RACGAP1, KIAA1478, MGCRACGAP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0H5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 100mM sodium cacodylate buffer, 13% polyethylene glycol 6000, 25% glycerol, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 0.97928 Å
DetectorDetector: CCD / Date: Nov 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 15787 / Num. obs: 15787 / % possible obs: 99.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 51.6
Reflection shellResolution: 1.9→1.93 Å / % possible obs: 98.3 % / Rmerge F obs: 0.485 / Mean I/σ(I) obs: 5.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OVJ

2ovj


Resolution: 1.9→25.31 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.909 / SU B: 3.941 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25873 784 5 %RANDOM
Rwork0.22158 ---
obs0.22346 14962 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.72 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 0 133 1717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191613
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9461.9852186
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4195199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95724.34869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82215300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3521511
X-RAY DIFFRACTIONr_chiral_restr0.0620.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211187
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 56 -
Rwork0.255 968 -
obs--97.9 %

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