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- PDB-4jgw: The conformation of a docking site for SH3 domains is pre-selecte... -

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Basic information

Entry
Database: PDB / ID: 4jgw
TitleThe conformation of a docking site for SH3 domains is pre-selected in the Guanine Nucleotide Exchange Factor Rlf
ComponentsRal guanine nucleotide dissociation stimulator-like 2
KeywordsSIGNALING PROTEIN / REM-domain / CDC25-homology domain / Guanine Nucleotide Exchange Factor / small G-protein binding / SH3 domain binding
Function / homology
Function and homology information


regulation of Ral protein signal transduction / RAF/MAP kinase cascade / negative regulation of cardiac muscle cell apoptotic process / small GTPase-mediated signal transduction / guanyl-nucleotide exchange factor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
Similarity search - Function
Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / Ras-associating (RA) domain ...Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Ubiquitin-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ral guanine nucleotide dissociation stimulator-like 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRehmann, H. / Popovic, M. / Jakobi, A.J.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: The guanine nucleotide exchange factor Rlf interacts with SH3 domain-containing proteins via a binding site with a preselected conformation.
Authors: Popovic, M. / Jakobi, A.J. / Rensen-de Leeuw, M. / Rehmann, H.
History
DepositionMar 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Ral guanine nucleotide dissociation stimulator-like 2
B: Ral guanine nucleotide dissociation stimulator-like 2


Theoretical massNumber of molelcules
Total (without water)104,2282
Polymers104,2282
Non-polymers00
Water3,279182
1
A: Ral guanine nucleotide dissociation stimulator-like 2


Theoretical massNumber of molelcules
Total (without water)52,1141
Polymers52,1141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ral guanine nucleotide dissociation stimulator-like 2


Theoretical massNumber of molelcules
Total (without water)52,1141
Polymers52,1141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.930, 75.620, 101.330
Angle α, β, γ (deg.)90.00, 98.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ral guanine nucleotide dissociation stimulator-like 2 / RalGDS-like 2 / RalGDS-like factor / Ras-associated protein RAB2L


Mass: 52113.898 Da / Num. of mol.: 2 / Fragment: UNP residues 50-514
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rgl2, Rab2l, Rlf / Plasmid: pGEX6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: Q61193
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON AND CDNA WAS OBTAINED FROM R. M. WOLTHUIS, ET AL., RALGDS LIKE FACTOR (RLF) ...THE SEQUENCE IS BASED ON AND CDNA WAS OBTAINED FROM R. M. WOLTHUIS, ET AL., RALGDS LIKE FACTOR (RLF) IS A NOVEL RAS AND RAP 1A-ASSOCIATING PROTEIN, 13(2), 353 (1996). THE EXPERIMENTAL INFO OF UNIPROT (Q61193 RGL2_MOUSE) SHOWS 147 H -> Y, 402 M -> T IN THIS REFERENCE.

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris propane, 0.2M NaNO3, 12% PEG 3350 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.3→31 Å / Num. all: 47332 / Num. obs: 46676 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.73 % / Net I/σ(I): 24.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.94 % / Mean I/σ(I) obs: 3.44 / Num. unique all: 5592 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QXL, 2IJE

3qxl

2ije


Resolution: 2.3→30.98 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.633 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28793 2335 5 %RANDOM
Rwork0.25156 ---
obs0.25337 44339 100 %-
all-47332 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.568 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å2-0.59 Å2
2---0.63 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6117 0 0 182 6299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226235
X-RAY DIFFRACTIONr_angle_refined_deg0.8871.9798477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9545780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.73622.657271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.799151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0891564
X-RAY DIFFRACTIONr_chiral_restr0.0530.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214700
X-RAY DIFFRACTIONr_mcbond_it0.2591.53950
X-RAY DIFFRACTIONr_mcangle_it0.48426338
X-RAY DIFFRACTIONr_scbond_it0.52432285
X-RAY DIFFRACTIONr_scangle_it0.9594.52139
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 169 -
Rwork0.287 3228 -
obs--100 %

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