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- PDB-2efd: Ara7/AtVps9a -

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Basic information

Entry
Database: PDB / ID: 2efd
TitleAra7/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 / intracellular organelle / embryo development ending in seed dormancy / molecular sequestering activity / vacuole organization / late endosome to vacuole transport / multivesicular body membrane / small molecule binding ...cell plate assembly / post-embryonic root development / cell wall biogenesis / intracellular organelle / embryo development ending in seed dormancy / molecular sequestering activity / vacuole organization / late endosome to vacuole transport / multivesicular body membrane / small molecule binding / GTPase activator activity / guanyl-nucleotide exchange factor activity / intracellular protein transport / early endosome membrane / early endosome / endosome / GTPase activity / GTP binding / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 ...Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / small GTPase Rab1 family profile. / Serum Albumin; Chain A, Domain 1 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / 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
Vacuolar protein sorting-associated protein 9A / Ras-related protein RABF2b
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsUejima, T. / Ihara, K. / 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: Version format compliance
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Mar 13, 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

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)100,1114
Polymers100,1114
Non-polymers00
Water0
1
A: Similarity to vacuolar protein sorting-associated protein VPS9
B: Small GTP-binding protein-like


Theoretical massNumber of molelcules
Total (without water)50,0562
Polymers50,0562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Similarity to vacuolar protein sorting-associated protein VPS9
D: Small GTP-binding protein-like


Theoretical massNumber of molelcules
Total (without water)50,0562
Polymers50,0562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.544, 189.544, 75.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3% PEG4000, 50mM imidazole malate, 50mM NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A10.9198
SYNCHROTRONSSRL BL9-220.97920, 0.91162, 0.97932
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDApr 23, 2005
MARMOSAIC 325 mm CCD2CCDApr 23, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91981
20.97921
30.911621
40.979321
ReflectionResolution: 3→100 Å / Num. obs: 29805 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Biso Wilson estimate: 100.3 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 27.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3→38.95 Å / Cor.coef. Fo:Fc: 0.844 / Cor.coef. Fo:Fc free: 0.805 / SU B: 22.755 / SU ML: 0.436 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.329 / ESU R Free: 0.513 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35126 1494 5 %RANDOM
Rwork0.30576 ---
obs0.30797 28248 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.663 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20.72 Å20 Å2
2--1.44 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 3→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 0 0 6266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226382
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9558618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6855790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35925.033302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.967151130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9551532
X-RAY DIFFRACTIONr_chiral_restr0.0850.2962
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024810
X-RAY DIFFRACTIONr_nbd_refined0.2270.23236
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0240.21
X-RAY DIFFRACTIONr_mcbond_it0.4281.54060
X-RAY DIFFRACTIONr_mcangle_it0.76526378
X-RAY DIFFRACTIONr_scbond_it0.74532587
X-RAY DIFFRACTIONr_scangle_it1.2734.52240
LS refinement shellResolution: 3.003→3.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 114 -
Rwork0.322 2109 -
obs--99.87 %

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