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- PDB-2gnc: Crystal structure of srGAP1 SH3 domain in the slit-robo signaling... -

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Basic information

Entry
Database: PDB / ID: 2gnc
TitleCrystal structure of srGAP1 SH3 domain in the slit-robo signaling pathway
ComponentsSLIT-ROBO Rho GTPase-activating protein 1
KeywordsSIGNALING PROTEIN / BETA BARREL
Function / homology
Function and homology information


: / small GTPase binding => GO:0031267 / small GTPase binding => GO:0031267 / Rho protein signal transduction / GTPase activator activity / negative regulation of cell migration / cell migration / cytoplasm
Similarity search - Function
SLIT-ROBO Rho GTPase-activating protein 1, F-BAR domain / 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 ...SLIT-ROBO Rho GTPase-activating protein 1, F-BAR domain / 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 / SH3 type barrels. / Src homology 3 domains / 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 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, X. / Liu, Y. / Gao, F. / Bartlam, M. / Wu, J.Y. / Rao, Z.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural Basis of Robo Proline-rich Motif Recognition by the srGAP1 Src Homology 3 Domain in the Slit-Robo Signaling Pathway
Authors: Li, X. / Chen, Y. / Liu, Y. / Gao, J. / Gao, F. / Bartlam, M. / Wu, J.Y. / Rao, Z.
History
DepositionApr 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: SLIT-ROBO Rho GTPase-activating protein 1
B: SLIT-ROBO Rho GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)13,5052
Polymers13,5052
Non-polymers00
Water3,081171
1
A: SLIT-ROBO Rho GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)6,7531
Polymers6,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SLIT-ROBO Rho GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)6,7531
Polymers6,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.321, 70.321, 70.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein SLIT-ROBO Rho GTPase-activating protein 1 / srGAP1 / Rho-GTPase- activating protein 13 / Fragment


Mass: 6752.610 Da / Num. of mol.: 2 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q91Z69
#2: 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M Lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 11938 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.81→1.87 Å

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Processing

Software
NameVersionClassification
CrystalCleardata collection
HKL-2000data reduction
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK2

1bk2


Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 495 RANDOM
Rwork0.208 --
all0.225 11029 -
obs0.225 9696 -
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 0 171 1073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011704
X-RAY DIFFRACTIONc_angle_deg1.60334

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