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- PDB-3kuq: Crystal structure of the DLC1 RhoGAP domain -

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Basic information

Entry
Database: PDB / ID: 3kuq
TitleCrystal structure of the DLC1 RhoGAP domain
ComponentsRho GTPase-activating protein 7
KeywordsHYDROLASE ACTIVATOR / Structural Genomics Consortium / GTPase activation / SGC / Alternative splicing / Cytoplasm / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


hindbrain morphogenesis / negative regulation of focal adhesion assembly / regulation of Rho protein signal transduction / focal adhesion assembly / regulation of small GTPase mediated signal transduction / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / cortical actin cytoskeleton / RHOB GTPase cycle / positive regulation of execution phase of apoptosis ...hindbrain morphogenesis / negative regulation of focal adhesion assembly / regulation of Rho protein signal transduction / focal adhesion assembly / regulation of small GTPase mediated signal transduction / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / cortical actin cytoskeleton / RHOB GTPase cycle / positive regulation of execution phase of apoptosis / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / heart morphogenesis / positive regulation of protein dephosphorylation / forebrain development / RAC1 GTPase cycle / SH2 domain binding / GTPase activator activity / negative regulation of cell migration / neural tube closure / caveola / regulation of actin cytoskeleton organization / ruffle membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of cell shape / actin cytoskeleton organization / membrane raft / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / focal adhesion / lipid binding / apoptotic process / endoplasmic reticulum / signal transduction / nucleus / cytosol / cytoplasm
Similarity search - Function
Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases ...Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / START-like domain superfamily / SAM domain (Sterile alpha motif) / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho GTPase-activating protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsNedyalkova, L. / Tempel, W. / Tong, Y. / MacKenzie, F. / Shen, L. / Zhong, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Nedyalkova, L. / Tempel, W. / Tong, Y. / MacKenzie, F. / Shen, L. / Zhong, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the DLC1 RhoGAP domain
Authors: Nedyalkova, L. / Tempel, W. / Tong, Y. / MacKenzie, F. / Shen, L. / Zhong, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionNov 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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: Rho GTPase-activating protein 7


Theoretical massNumber of molelcules
Total (without water)26,0395
Polymers26,0391
Non-polymers04
Water54030
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.577, 97.502, 92.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2-

UNX

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Components

#1: Protein Rho GTPase-activating protein 7 / Rho-type GTPase-activating protein 7 / Deleted in liver cancer 1 protein / Dlc-1 / StAR-related ...Rho-type GTPase-activating protein 7 / Deleted in liver cancer 1 protein / Dlc-1 / StAR-related lipid transfer protein 12 / START domain-containing protein 12 / StARD12 / HP protein


Mass: 26038.930 Da / Num. of mol.: 1 / Fragment: Rho-GAP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLC1, ARHGAP7, KIAA1723, STARD12 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q96QB1
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 30% PEG-3350, 0.2M sodium chloride, 5% glycerol, 0.02M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915
DetectorType: ADSC Q315 / Detector: CCD / Date: Nov 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 12307 / % possible obs: 98.2 %
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.685 / % possible all: 87.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3fk2

3fk2


Resolution: 2.3→48.75 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.188 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The programs CHAINSAW, PHENIX, ARP/WARP, COOT and MOLPROBITY were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.26028 584 4.8 %RANDOM
Rwork0.21615 ---
obs0.21821 11699 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2--1.96 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 4 30 1542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221534
X-RAY DIFFRACTIONr_bond_other_d0.0020.021011
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9742083
X-RAY DIFFRACTIONr_angle_other_deg0.91632480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2725.13574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14415264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.561159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02291
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_it0.7211.5962
X-RAY DIFFRACTIONr_mcbond_other0.1511.5383
X-RAY DIFFRACTIONr_mcangle_it1.42121546
X-RAY DIFFRACTIONr_scbond_it2.4183572
X-RAY DIFFRACTIONr_scangle_it4.1014.5536
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 36 -
Rwork0.259 765 -
obs--89.2 %

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