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- PDB-2efe: Ara7-GDPNH2/AtVps9a -

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Basic information

Entry
Database: PDB / ID: 2efe
TitleAra7-GDPNH2/AtVps9a
Components
  • Similarity to vacuolar protein sorting-associated protein VPS9
  • Small GTP-binding protein-like
KeywordsTRANSPORT PROTEIN / GEF / GTPase / Vps9 / Rab5 / nucleotide
Function / homology
Function and homology information


cell plate assembly / post-embryonic root development / cell wall biogenesis / embryo development ending in seed dormancy / multivesicular body membrane / intracellular organelle / vacuole organization / late endosome to vacuole transport / endocytic vesicle / endomembrane system ...cell plate assembly / post-embryonic root development / cell wall biogenesis / embryo development ending in seed dormancy / multivesicular body membrane / intracellular organelle / vacuole organization / late endosome to vacuole transport / endocytic vesicle / endomembrane system / GTPase activator activity / guanyl-nucleotide exchange factor activity / intracellular protein transport / positive regulation of GTPase activity / early endosome membrane / early endosome / endosome / GTPase activity / GTP binding / endoplasmic reticulum / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / Domain of unknown function (DUF5601) / RABX5, catalytic core helical domain / VPS9 domain superfamily / VPS9 domain profile. / Vacuolar sorting protein 9 (VPS9) domain / Domain present in VPS9 / VPS9 domain / small GTPase Rab1 family profile. ...Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / Domain of unknown function (DUF5601) / RABX5, catalytic core helical domain / VPS9 domain superfamily / VPS9 domain profile. / Vacuolar sorting protein 9 (VPS9) domain / Domain present in VPS9 / VPS9 domain / small GTPase Rab1 family profile. / Serum Albumin; Chain A, Domain 1 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Ras family / Small GTPase / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AMINOPHOSPHONIC ACID-GUANYLATE ESTER / Vacuolar protein sorting-associated protein 9A / Ras-related protein RABF2b
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsIhara, K. / Uejima, T. / Wakatsuki, S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5/Vps9 system
Authors: Uejima, T. / Ihara, K. / Goh, T. / Ito, E. / Sunada, M. / Ueda, T. / Nakano, A. / Wakatsuki, S.
History
DepositionFeb 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Dec 21, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Similarity to vacuolar protein sorting-associated protein VPS9
B: Small GTP-binding protein-like
C: Similarity to vacuolar protein sorting-associated protein VPS9
D: Small GTP-binding protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9966
Polymers100,1114
Non-polymers8842
Water5,873326
1
A: Similarity to vacuolar protein sorting-associated protein VPS9
B: Small GTP-binding protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4983
Polymers50,0562
Non-polymers4421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-18 kcal/mol
Surface area19080 Å2
MethodPISA, PQS
2
C: Similarity to vacuolar protein sorting-associated protein VPS9
D: Small GTP-binding protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4983
Polymers50,0562
Non-polymers4421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-19 kcal/mol
Surface area19080 Å2
MethodPISA, PQS
Unit cell
γ
α
β
Length a, b, c (Å)58.235, 58.296, 69.243
Angle α, β, γ (deg.)81.75, 86.83, 73.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Similarity to vacuolar protein sorting-associated protein VPS9 / AtVps9a / Hypothetical protein At3g19770


Mass: 30168.316 Da / Num. of mol.: 2 / Fragment: Vps9 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami(DE3)pLysS / References: UniProt: Q9LT31
#2: Protein Small GTP-binding protein-like / Ara7 / AT4g19640/F24J7_190


Mass: 19887.432 Da / Num. of mol.: 2 / Fragment: GTPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9SN68
#3: Chemical ChemComp-GNH / AMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 442.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N6O10P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 200mM lithium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→100 Å / Num. obs: 49631 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 11.3
Reflection shellResolution: 2.08→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.4 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: nucleotide-free Ara7/AtVps9a which was solved by MAD

Resolution: 2.08→68.52 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.764 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.288 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28178 2529 5.1 %RANDOM
Rwork0.22695 ---
obs0.22977 47099 95.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.447 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20.26 Å20.27 Å2
2--0.11 Å20.2 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.08→68.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 56 326 6862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226662
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9649010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.58725.127316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1821532
X-RAY DIFFRACTIONr_chiral_restr0.1090.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025014
X-RAY DIFFRACTIONr_nbd_refined0.220.23337
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24590
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2410
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.212
X-RAY DIFFRACTIONr_mcbond_it0.7321.54191
X-RAY DIFFRACTIONr_mcangle_it1.27626592
X-RAY DIFFRACTIONr_scbond_it1.77332783
X-RAY DIFFRACTIONr_scangle_it2.8554.52418
LS refinement shellResolution: 2.082→2.136 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 148 -
Rwork0.32 2825 -
obs--78.44 %

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