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- PDB-5xr6: Crystal structure of RabA1a in complex with GppNHp -

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Basic information

Entry
Database: PDB / ID: 5xr6
TitleCrystal structure of RabA1a in complex with GppNHp
ComponentsRas-related protein RABA1a
KeywordsPROTEIN TRANSPORT / GTPase / G-protein / Cellular transportation / Arabidopsis thaliana
Function / homology
Function and homology information


cell wall biogenesis / response to auxin / vesicle-mediated transport / protein transport / endosome / GTPase activity / GTP binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / 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 protein RABA1a
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsYun, J.S. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation2013R1A1A1061391 and 2016R1C1B2009691 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure and subcellular localization of RabA1a from Arabidopsis thaliana
Authors: Yun, J.S. / Ha, S.C. / Kim, Y.G. / Kim, H.R. / Chang, J.H.
History
DepositionJun 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein RABA1a
B: Ras-related protein RABA1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7516
Polymers43,6582
Non-polymers1,0934
Water73941
1
A: Ras-related protein RABA1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3753
Polymers21,8291
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-14 kcal/mol
Surface area9020 Å2
MethodPISA
2
B: Ras-related protein RABA1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3753
Polymers21,8291
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-13 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.634, 48.416, 68.508
Angle α, β, γ (deg.)88.53, 74.15, 84.37
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ras-related protein RABA1a / AtRABA1a / Ras-related protein Ara-2 / Ras-related protein Rab11E / AtRab11E


Mass: 21828.830 Da / Num. of mol.: 2 / Fragment: UNP residues 10-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RABA1A, ARA-2, RAB11E, At1g06400, T2D23.10, T2D23_5 / Production host: Escherichia coli (E. coli) / References: UniProt: P28185
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES (pH5.5), 10 mM magnesium acetate, 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14606 / % possible obs: 96.5 % / Redundancy: 3 % / Net I/σ(I): 28.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.6→27.183 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.8
RfactorNum. reflection% reflection
Rfree0.2653 1372 10 %
Rwork0.2033 --
obs0.2092 13721 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→27.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2676 0 66 41 2783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082788
X-RAY DIFFRACTIONf_angle_d1.1273782
X-RAY DIFFRACTIONf_dihedral_angle_d16.6961638
X-RAY DIFFRACTIONf_chiral_restr0.058438
X-RAY DIFFRACTIONf_plane_restr0.005462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69290.39321410.25971262X-RAY DIFFRACTION96
2.6929-2.80060.34251360.25721224X-RAY DIFFRACTION98
2.8006-2.92790.29061440.22921263X-RAY DIFFRACTION98
2.9279-3.0820.31421390.2161248X-RAY DIFFRACTION98
3.082-3.27480.29521430.21931260X-RAY DIFFRACTION98
3.2748-3.52720.28641340.19581235X-RAY DIFFRACTION98
3.5272-3.88120.25791380.19631260X-RAY DIFFRACTION98
3.8812-4.44080.2471390.17811238X-RAY DIFFRACTION97
4.4408-5.58690.22741370.18221231X-RAY DIFFRACTION97
5.5869-27.18480.22021210.21121128X-RAY DIFFRACTION87

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