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- PDB-5xr4: Crystal structure of RabA1a in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 5xr4
TitleCrystal structure of RabA1a in complex with GDP
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 / protein transport / endosome / GTPase activity / GTP binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
small GTPase Rab1 family profile. / 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 / P-loop containing nucleoside triphosphate hydrolase ...small GTPase Rab1 family profile. / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein RABA1a
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 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
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_src_syn / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)44,7858
Polymers43,6582
Non-polymers1,1276
Water27015
1
A: Ras-related protein RABA1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3924
Polymers21,8291
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-29 kcal/mol
Surface area7970 Å2
MethodPISA
2
B: Ras-related protein RABA1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3924
Polymers21,8291
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-39 kcal/mol
Surface area8450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.708, 70.407, 68.040
Angle α, β, γ (deg.)90.00, 97.21, 90.00
Int Tables number4
Space group name H-MP1211

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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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 15 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis Tris (pH5.5), 0.2 M Ammonium sulfate, 26% PEG 3350

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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: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 8840 / % possible obs: 99.5 % / Redundancy: 4.2 % / Net I/σ(I): 19.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.8→27.981 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.09
RfactorNum. reflection% reflection
Rfree0.2694 853 10.01 %
Rwork0.1848 --
obs0.1931 8519 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→27.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 56 12 15 2651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082678
X-RAY DIFFRACTIONf_angle_d1.0993633
X-RAY DIFFRACTIONf_dihedral_angle_d18.121572
X-RAY DIFFRACTIONf_chiral_restr0.057421
X-RAY DIFFRACTIONf_plane_restr0.004443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.97530.36371410.22911262X-RAY DIFFRACTION100
2.9753-3.20480.32111410.2211269X-RAY DIFFRACTION100
3.2048-3.52670.29491430.19641287X-RAY DIFFRACTION100
3.5267-4.03570.2551420.18121275X-RAY DIFFRACTION100
4.0357-5.07960.28491420.15571278X-RAY DIFFRACTION99
5.0796-27.98210.2071440.17891295X-RAY DIFFRACTION99

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