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- PDB-3wpq: crystal structure of the GAP domain of MgcRacGAP(S387A) -

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Basic information

Entry
Database: PDB / ID: 3wpq
Titlecrystal structure of the GAP domain of MgcRacGAP(S387A)
ComponentsRac GTPase-activating protein 1
KeywordsSIGNALING PROTEIN / GTPase activation / small G-proteins
Function / homology
Function and homology information


centralspindlin complex / sulfate transport / actomyosin contractile ring assembly / mitotic spindle midzone assembly / regulation of attachment of spindle microtubules to kinetochore / gamma-tubulin binding / Kinesins / RHOD GTPase cycle / Flemming body / regulation of small GTPase mediated signal transduction ...centralspindlin complex / sulfate transport / actomyosin contractile ring assembly / mitotic spindle midzone assembly / regulation of attachment of spindle microtubules to kinetochore / gamma-tubulin binding / Kinesins / RHOD GTPase cycle / 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 / mitotic cytokinesis / CDC42 GTPase cycle / Rho protein signal transduction / 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 / cytoplasmic side of plasma membrane / mitotic spindle / spindle / 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
Rac GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Shirouzu, M. / Kitamura, T. / Yokoyama, S.
CitationJournal: To be Published
Title: crystal structure of the GAP domain of MgcRacGAP
Authors: Murayama, K. / Kato-Murayama, M. / Shirouzu, M. / Kitamura, T. / Yokoyama, S.
History
DepositionJan 15, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Rac GTPase-activating protein 1
B: Rac GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)46,3542
Polymers46,3542
Non-polymers00
Water9,926551
1
A: Rac GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)23,1771
Polymers23,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rac GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)23,1771
Polymers23,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.960, 53.610, 86.388
Angle α, β, γ (deg.)90.00, 97.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rac GTPase-activating protein 1 / Male germ cell RacGap / MgcRacGAP / Protein CYK4 homolog / CYK4 / HsCYK-4


Mass: 23176.887 Da / Num. of mol.: 2 / Fragment: UNP residues 346-546 / Mutation: S387A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PLASMID pCR2.1 / Gene: RACGAP1, KIAA1478, MGCRACGAP / Production host: cell-free protein synthesis (unknown) / References: UniProt: Q9H0H5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE ACCESSION NUMBER BAA90247.1 IN THE GENEBANK.

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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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.0M Na Citrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 38896 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.075 / Net I/σ(I): 17.1
Reflection shellResolution: 1.84→1.91 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.432 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OVJ

2ovj


Resolution: 1.84→28.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1027008.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1943 5 %RANDOM
Rwork0.167 ---
obs0.167 38801 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.8917 Å2 / ksol: 0.390357 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å21.29 Å2
2--2.3 Å20 Å2
3----3.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.84→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 551 3689
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 1.84→1.96 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 315 4.9 %
Rwork0.235 6125 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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