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- PDB-5i7d: Crystal Structure of srGAP2 F-BARx WT Form-2 -

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Basic information

Entry
Database: PDB / ID: 5i7d
TitleCrystal Structure of srGAP2 F-BARx WT Form-2
ComponentsSLIT-ROBO Rho GTPase-activating protein 2
KeywordsSIGNALING PROTEIN / srGAP2 / F-BAR / Fx
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 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
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: 3.95 Å
AuthorsSporny, M. / Guez-Haddad, J. / Isupov, M.N. / Opatowsky, Y.
Funding support Israel, 2items
OrganizationGrant numberCountry
ISF182/10 and 1425/15 Israel
BSF2013310 Israel
CitationJournal: To Be Published
Title: Structural Basis for srGAP2 Membrane Interactions, and Antagonism by the Human Specific Paralog srGAP2C
Authors: Sporny, M. / Guez-Haddad, J. / Isupov, M.N. / Opatowsky, Y.
History
DepositionFeb 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Dec 11, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list

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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


Theoretical massNumber of molelcules
Total (without water)113,1102
Polymers113,1102
Non-polymers00
Water0
1
A: SLIT-ROBO Rho GTPase-activating protein 2

A: SLIT-ROBO Rho GTPase-activating protein 2


Theoretical massNumber of molelcules
Total (without water)113,1102
Polymers113,1102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17180 Å2
ΔGint-123 kcal/mol
Surface area43410 Å2
MethodPISA
2
B: SLIT-ROBO Rho GTPase-activating protein 2

B: SLIT-ROBO Rho GTPase-activating protein 2


Theoretical massNumber of molelcules
Total (without water)113,1102
Polymers113,1102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17070 Å2
ΔGint-123 kcal/mol
Surface area43510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.904, 49.926, 234.084
Angle α, β, γ (deg.)90.00, 102.57, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A8 - 481
2010B8 - 481

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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: 56555.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRGAP2, ARHGAP34, FNBP2, KIAA0456, SRGAP2A / Production host: Homo sapiens (human) / References: UniProt: O75044

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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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: F-BARx eluted in 5% Glycerol, 25 mM Tris buffer pH=8.5, 1 mM DTT, and ~0.2 M NaCl at the elution peak, concentrated to ~15 mg/ml and crystallized in 0.2 M Ammonium citrate tribasic pH 6.5, 0. ...Details: F-BARx eluted in 5% Glycerol, 25 mM Tris buffer pH=8.5, 1 mM DTT, and ~0.2 M NaCl at the elution peak, concentrated to ~15 mg/ml and crystallized in 0.2 M Ammonium citrate tribasic pH 6.5, 0.2 M Guanidine, 0.3 M NaCl, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.008818 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008818 Å / Relative weight: 1
ReflectionResolution: 3.95→50 Å / Num. obs: 12297 / % possible obs: 98.2 % / Redundancy: 3.6 % / Net I/σ(I): 8.32

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.95→46.39 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.877 / SU B: 97.94 / SU ML: 1.102 / Cross valid method: THROUGHOUT / ESU R Free: 1.068
RfactorNum. reflection% reflectionSelection details
Rfree0.34941 615 5 %RANDOM
Rwork0.27689 ---
obs0.28037 11681 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 196.854 Å2
Baniso -1Baniso -2Baniso -3
1--6.27 Å20 Å2-4.64 Å2
2--31.69 Å20 Å2
3----21.24 Å2
Refinement stepCycle: 1 / Resolution: 3.95→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6702 0 0 0 6702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196792
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9719094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9185808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg51.21825.81358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.992151400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2451538
X-RAY DIFFRACTIONr_chiral_restr0.0720.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024986
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_it5.32819.53262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it9.12129.2384054
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.08219.683530
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined20.08926727
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1136 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.942→4.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 43 -
Rwork0.454 820 -
obs--93.2 %

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