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- PDB-2ovj: The crystal structure of the human Rac GTPase activating protein ... -

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Basic information

Entry
Database: PDB / ID: 2ovj
TitleThe crystal structure of the human Rac GTPase activating protein 1 (RACGAP1) MgcRacGAP.
ComponentsRac GTPase-activating protein 1
KeywordsSIGNALING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC
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 / Kinesins / Flemming body / 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 / Kinesins / Flemming body / 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 / neuroblast proliferation / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / monoatomic ion transport / RAC1 GTPase cycle / MHC class II antigen presentation / GTPase activator activity / erythrocyte differentiation / acrosomal vesicle / mitotic spindle / cytoplasmic side of plasma membrane / spindle / protein-macromolecule adaptor activity / midbody / microtubule binding / spermatogenesis / microtubule / protein kinase binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / 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
Chem-7PE / Rac GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsShrestha, L. / Papagrigoriou, E. / Soundararajan, M. / Elkins, J. / Johansson, C. / von Delft, F. / Pike, A.C.W. / Burgess, N. / Turnbull, A. / Debreczeni, J. ...Shrestha, L. / Papagrigoriou, E. / Soundararajan, M. / Elkins, J. / Johansson, C. / von Delft, F. / Pike, A.C.W. / Burgess, N. / Turnbull, A. / Debreczeni, J. / Gorrec, F. / Umeano, C. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of the human Rac GTPase activating protein 1 (RACGAP1) MgcRacGAP.
Authors: Shrestha, L. / Papagrigoriou, E. / Soundararajan, M. / Elkins, J. / Johansson, C. / von Delft, F. / Pike, A.C.W. / Burgess, N. / Turnbull, A. / Debreczeni, J. / Gorrec, F. / Umeano, C. / ...Authors: Shrestha, L. / Papagrigoriou, E. / Soundararajan, M. / Elkins, J. / Johansson, C. / von Delft, F. / Pike, A.C.W. / Burgess, N. / Turnbull, A. / Debreczeni, J. / Gorrec, F. / Umeano, C. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Doyle, D.A.
History
DepositionFeb 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rac GTPase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0582
Polymers22,7481
Non-polymers3101
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.913, 53.548, 67.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer

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Components

#1: Protein Rac GTPase-activating protein 1 / MgcRacGAP


Mass: 22747.562 Da / Num. of mol.: 1 / Fragment: Rho-GAP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RACGAP1, KIAA1478, MGCRACGAP / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H0H5
#2: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT / Polyethylene glycol


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 41.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→42.07 Å / Num. all: 32274 / Num. obs: 32274 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.491 / Num. unique all: 3134 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F7C

1f7c


Resolution: 1.49→42.07 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.956 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17611 1631 5.1 %RANDOM
Rwork0.15188 ---
all0.15307 30586 --
obs0.15307 30586 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.767 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.49→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 16 171 1749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221657
X-RAY DIFFRACTIONr_bond_other_d0.0030.021126
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9872256
X-RAY DIFFRACTIONr_angle_other_deg1.0532781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.5185212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95623.88167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96915300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4151512
X-RAY DIFFRACTIONr_chiral_restr0.1120.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
X-RAY DIFFRACTIONr_nbd_refined0.2420.2374
X-RAY DIFFRACTIONr_nbd_other0.1960.21235
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2860
X-RAY DIFFRACTIONr_nbtor_other0.0880.2810
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.18331067
X-RAY DIFFRACTIONr_mcbond_other0.5783401
X-RAY DIFFRACTIONr_mcangle_it2.91251704
X-RAY DIFFRACTIONr_scbond_it3.9287652
X-RAY DIFFRACTIONr_scangle_it5.70511546
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 121 -
Rwork0.195 2156 -
obs--98.02 %
Refinement TLS params.Method: refined / Origin x: 13.3898 Å / Origin y: 1.8942 Å / Origin z: 12.3309 Å
111213212223313233
T-0.0183 Å20.002 Å2-0.0017 Å2--0.0084 Å2-0.0001 Å2---0.0161 Å2
L0.2701 °20.0903 °2-0.1228 °2-0.3505 °2-0.0199 °2--0.3562 °2
S-0.0132 Å °-0.0013 Å °0.0225 Å °-0.0101 Å °0.0109 Å °-0.0041 Å °0.0126 Å °0.0018 Å °0.0023 Å °

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