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- PDB-4rtt: Cyrstal structure of SLIT-ROBO Rho GTPase-activating protein 2 fr... -

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Basic information

Entry
Database: PDB / ID: 4rtt
TitleCyrstal structure of SLIT-ROBO Rho GTPase-activating protein 2 fragment
ComponentsSLIT-ROBO Rho GTPase-activating protein 2
KeywordsPROTEIN BINDING / srGAP2 / SH3 / Ligand binding / Robo1 / Nuclear / Plasma Membrane
Function / homology
Function and homology information


lamellipodium assembly involved in ameboidal cell migration / extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration / excitatory synapse assembly / negative regulation of neuron migration / Inactivation of CDC42 and RAC1 / inhibitory synapse assembly / dendritic spine development / actin filament severing / filopodium assembly / RHOF GTPase cycle ...lamellipodium assembly involved in ameboidal cell migration / extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration / excitatory synapse assembly / negative regulation of neuron migration / Inactivation of CDC42 and RAC1 / inhibitory synapse assembly / dendritic spine development / actin filament severing / filopodium assembly / RHOF GTPase cycle / regulation of small GTPase mediated signal transduction / dendritic spine head / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / RAC3 GTPase cycle / phagocytic vesicle / RAC1 GTPase cycle / GTPase activator activity / substrate adhesion-dependent cell spreading / negative regulation of cell migration / neuron projection morphogenesis / RHO GTPases Activate Formins / small GTPase binding / positive regulation of GTPase activity / lamellipodium / postsynaptic membrane / postsynaptic density / signal transduction / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
srGAP1/2/3, SH3 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. ...srGAP1/2/3, SH3 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
SLIT-ROBO Rho GTPase-activating protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsOpatowsky, Y. / Guez-Hadad, J.
CitationJournal: Structure / Year: 2015
Title: The Neuronal Migration Factor srGAP2 Achieves Specificity in Ligand Binding through a Two-Component Molecular Mechanism.
Authors: Guez-Haddad, J. / Sporny, M. / Sasson, Y. / Gevorkyan-Airapetov, L. / Lahav-Mankovski, N. / Margulies, D. / Radzimanowski, J. / Opatowsky, Y.
History
DepositionNov 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: SLIT-ROBO Rho GTPase-activating protein 2
B: SLIT-ROBO Rho GTPase-activating protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8315
Polymers20,5432
Non-polymers2883
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SLIT-ROBO Rho GTPase-activating protein 2
hetero molecules

B: SLIT-ROBO Rho GTPase-activating protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8315
Polymers20,5432
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
Buried area1220 Å2
ΔGint-31 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.300, 52.540, 92.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 728 - 809 / Label seq-ID: 5 - 86

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein SLIT-ROBO Rho GTPase-activating protein 2 / srGAP2 / Formin-binding protein 2 / Rho GTPase-activating protein 34


Mass: 10271.398 Da / Num. of mol.: 2 / Fragment: UNP residues 729-815
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRGAP2, ARHGAP34, FNBP2, KIAA0456, SRGAP2A / Production host: Escherichia coli (E. coli) / References: UniProt: O75044
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.85 Å3/Da / Density % sol: 33.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.25
Details: 2.35M Ammonium Sulphate; 0.1M MES, pH 6.25, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.87→46.26 Å / Num. all: 13161 / Num. obs: 12959 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.103
Reflection shellResolution: 1.87→1.99 Å / % possible all: 94

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Processing

Software
NameVersionClassification
EDNAdata collection
BALBESphasing
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→46.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.307 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25944 648 5 %RANDOM
Rwork0.22101 ---
all0.22 13161 --
obs0.22299 12311 98.38 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.982 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å20 Å2
2--1.11 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.87→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 15 71 1366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191320
X-RAY DIFFRACTIONr_bond_other_d0.0040.021224
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.971787
X-RAY DIFFRACTIONr_angle_other_deg1.00532831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0795156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52324.15465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22215224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8381510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211456
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02286
X-RAY DIFFRACTIONr_mcbond_it1.7551.236636
X-RAY DIFFRACTIONr_mcbond_other1.7531.233635
X-RAY DIFFRACTIONr_mcangle_it2.9141.81788
X-RAY DIFFRACTIONr_mcangle_other2.9131.813789
X-RAY DIFFRACTIONr_scbond_it2.4091.599684
X-RAY DIFFRACTIONr_scbond_other2.0141.487670
X-RAY DIFFRACTIONr_scangle_other3.3542.162981
X-RAY DIFFRACTIONr_long_range_B_refined6.42310.2121400
X-RAY DIFFRACTIONr_long_range_B_other6.129.7881376
Refine LS restraints NCS

Ens-ID: 1 / Number: 4312 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.873→1.921 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 41 -
Rwork0.385 789 -
obs--87.92 %

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