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- PDB-2q3f: X-ray crystal structure of putative human Ras-related GTP binding... -

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Basic information

Entry
Database: PDB / ID: 2q3f
TitleX-ray crystal structure of putative human Ras-related GTP binding D in complex with GMPPNP
ComponentsRas-related GTP-binding protein D
KeywordsPROTEIN BINDING / Structural Genomics / GTP-binding / RRAGD / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Ragulator complex => GO:0071986 / regulation of cell cycle => GO:0051726 / protein localization => GO:0008104 / Gtr1-Gtr2 GTPase complex / cellular response to leucine starvation / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / Macroautophagy ...Ragulator complex => GO:0071986 / regulation of cell cycle => GO:0051726 / protein localization => GO:0008104 / Gtr1-Gtr2 GTPase complex / cellular response to leucine starvation / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / Macroautophagy / mTORC1-mediated signalling / positive regulation of TOR signaling / regulation of macroautophagy / positive regulation of TORC1 signaling / cellular response to starvation / Regulation of PTEN gene transcription / regulation of autophagy / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GDP binding / GTPase binding / lysosome / protein heterodimerization activity / GTPase activity / centrosome / GTP binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Gtr1/RagA G protein / RagC/D / Gtr1/RagA G protein conserved region / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related GTP-binding protein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMulichak, A.M. / Rabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Keefe, L.J. ...Mulichak, A.M. / Rabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Keefe, L.J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal structure of human Ras-related GTP-binding D.
Authors: Mulichak, A.M. / Rabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Keefe, L.J. / Bochkarev, A. / Park, H.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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: Ras-related GTP-binding protein D
B: Ras-related GTP-binding protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3466
Polymers42,2532
Non-polymers1,0934
Water1,62190
1
A: Ras-related GTP-binding protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6733
Polymers21,1261
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related GTP-binding protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6733
Polymers21,1261
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.730, 67.130, 66.360
Angle α, β, γ (deg.)90.00, 110.92, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Ras-related GTP-binding protein D / Rag D


Mass: 21126.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRAGD / Plasmid: p28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9NQL2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.4
Details: 31% PEG4000, 0.2M sodium acetate and 0.1M Tris HCl, pH 8.4, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97942, 1.0
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 14, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
211
ReflectionResolution: 2.05→50 Å / Num. all: 24803 / Num. obs: 24803 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 4.1 % / Rsym value: 0.054
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2438 / % possible all: 99.1

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Processing

Software
NameVersionClassification
JDirectordata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1065 -random
Rwork0.221 ---
all0.223 22965 --
obs0.223 21895 95.3 %-
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 66 90 3032
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d23.12
X-RAY DIFFRACTIONc_improper_angle_d0.81

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