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- PDB-2dtc: Crystal structure of MS0666 -

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Basic information

Entry
Database: PDB / ID: 2dtc
TitleCrystal structure of MS0666
ComponentsRAL GUANINE NUCLEOTIDE EXCHANGE FACTOR RALGPS1A
KeywordsPROTEIN BINDING / PH domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of Ral protein signal transduction / small GTPase-mediated signal transduction / guanyl-nucleotide exchange factor activity / plasma membrane / cytoplasm
Similarity search - Function
Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain ...Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Ras-specific guanine nucleotide-releasing factor RalGPS1 / Ras-specific guanine nucleotide-releasing factor RalGPS1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsWang, H. / Kishishita, S. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of MS0666
Authors: Wang, H. / Kishishita, S. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJul 12, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAL GUANINE NUCLEOTIDE EXCHANGE FACTOR RALGPS1A
B: RAL GUANINE NUCLEOTIDE EXCHANGE FACTOR RALGPS1A


Theoretical massNumber of molelcules
Total (without water)29,1772
Polymers29,1772
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-7 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.680, 61.077, 43.939
Angle α, β, γ (deg.)90.00, 104.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RAL GUANINE NUCLEOTIDE EXCHANGE FACTOR RALGPS1A


Mass: 14588.295 Da / Num. of mol.: 2 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CELL-FREE PROTEIN SYNTHESIS / Plasmid: PX051128-20 / References: UniProt: Q8BVR9, UniProt: A2AR50*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 1.94 Å3/Da / Density % sol: 36.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, TRIS, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9700, 0.9790, 0.9794
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 20, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
20.9791
30.97941
ReflectionResolution: 1.7→50 Å / Num. obs: 24140 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.072 / Net I/σ(I): 13.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 2370 / Rsym value: 0.269 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→34.75 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 187438.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1114 4.8 %RANDOM
Rwork0.192 ---
obs0.192 23256 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.9778 Å2 / ksol: 0.369065 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å2-4.07 Å2
2--4.24 Å20 Å2
3----1.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 0 288 2161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 155 4.5 %
Rwork0.247 3298 -
obs--84.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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