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- PDB-3qxl: Crystal structure of the CDC25 Domain from Ral-specific Guanine-n... -

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Basic information

Entry
Database: PDB / ID: 3qxl
TitleCrystal structure of the CDC25 Domain from Ral-specific Guanine-nucleotide Exchange Factor RalGPS1a
ComponentsRas-specific guanine nucleotide-releasing factor RalGPS1
KeywordsSIGNALING PROTEIN / Cdc25 domain homology / Guanine-nucleotide Exchange Factor / Small GTPase Ral subfamily
Function / homology
Function and homology information


regulation of Ral protein signal transduction / guanyl-nucleotide exchange factor activity / Ras protein signal transduction / intracellular signal transduction / plasma membrane / cytoplasm
Similarity search - Function
Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras-like guanine nucleotide exchange factor / 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 / PH domain ...Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras-like guanine nucleotide exchange factor / 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 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ras-specific guanine nucleotide-releasing factor RalGPS1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.237 Å
AuthorsPeng, W. / Xu, J. / Guan, X. / Sun, Y. / Li, X. / Zhang, X.C. / Rao, Z.
CitationJournal: Protein Cell / Year: 2011
Title: Structural study of the Cdc25 domain from Ral-specific guanine-nucleotide exchange factor RalGPS1a.
Authors: Peng, W. / Xu, J. / Guan, X. / Sun, Y. / Zhang, X.C. / Li, X. / Rao, Z.
History
DepositionMar 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Ras-specific guanine nucleotide-releasing factor RalGPS1
B: Ras-specific guanine nucleotide-releasing factor RalGPS1


Theoretical massNumber of molelcules
Total (without water)62,3022
Polymers62,3022
Non-polymers00
Water2,234124
1
A: Ras-specific guanine nucleotide-releasing factor RalGPS1


Theoretical massNumber of molelcules
Total (without water)31,1511
Polymers31,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-specific guanine nucleotide-releasing factor RalGPS1


Theoretical massNumber of molelcules
Total (without water)31,1511
Polymers31,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.504, 102.035, 82.141
Angle α, β, γ (deg.)90.00, 96.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ras-specific guanine nucleotide-releasing factor RalGPS1 / Ral GEF with PH domain and SH3-binding motif 1 / Ral guanine nucleotide exchange factor 2 / RalGEF ...Ral GEF with PH domain and SH3-binding motif 1 / Ral guanine nucleotide exchange factor 2 / RalGEF 2 / RalA exchange factor RalGPS1


Mass: 31150.912 Da / Num. of mol.: 2 / Fragment: UNP residues 23-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALGPS1, KIAA0351, RALGEF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JS13
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM KCl, 10 mM MgCl2, 50 mM sodium cacodylate and 8.5% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.237→40.8 Å / Num. obs: 28948 / % possible obs: 74 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.237→40.8 Å / SU ML: 0.28 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 1394 5.08 %Random
Rwork0.1968 ---
obs0.199 27464 94.91 %-
all-28948 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.269 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5797 Å2-0 Å20.264 Å2
2--0.0955 Å2-0 Å2
3---0.4842 Å2
Refinement stepCycle: LAST / Resolution: 2.237→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 0 124 4136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064096
X-RAY DIFFRACTIONf_angle_d0.8985537
X-RAY DIFFRACTIONf_dihedral_angle_d18.3871538
X-RAY DIFFRACTIONf_chiral_restr0.06639
X-RAY DIFFRACTIONf_plane_restr0.004688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.237-2.31650.28861200.23322031X-RAY DIFFRACTION74
2.3165-2.40930.32341220.23532440X-RAY DIFFRACTION88
2.4093-2.51890.26811520.21942549X-RAY DIFFRACTION94
2.5189-2.65170.24971300.21552651X-RAY DIFFRACTION97
2.6517-2.81780.23811480.20212702X-RAY DIFFRACTION99
2.8178-3.03530.26351180.19492748X-RAY DIFFRACTION99
3.0353-3.34060.23481490.19672712X-RAY DIFFRACTION99
3.3406-3.82370.19131460.17132708X-RAY DIFFRACTION100
3.8237-4.81630.20031490.16262758X-RAY DIFFRACTION100
4.8163-40.81010.23721600.18992771X-RAY DIFFRACTION100

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