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- PDB-3bwd: Crystal structure of the plant Rho protein ROP5 -

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Basic information

Entry
Database: PDB / ID: 3bwd
TitleCrystal structure of the plant Rho protein ROP5
ComponentsRac-like GTP-binding protein ARAC6
KeywordsPLANT PROTEIN / G domain / Cytoplasm / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Prenylation / ----
Function / homology
Function and homology information


small GTPase-mediated signal transduction / GTPase activity / GTP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Small GTPase Rho / small GTPase Rho family profile. / 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 / Rossmann fold ...Small GTPase Rho / small GTPase Rho family profile. / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Rac-like GTP-binding protein ARAC6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsThomas, C. / Berken, A.
Citation
Journal: To be Published
Title: Crystal structure of the plant Rho protein ROP5
Authors: Thomas, C. / Berken, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Purification, crystallization and preliminary X-ray diffraction analysis of the plant Rho protein ROP5
Authors: Thomas, C. / Berken, A.
History
DepositionJan 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Rac-like GTP-binding protein ARAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2793
Polymers19,8121
Non-polymers4682
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.420, 40.390, 57.180
Angle α, β, γ (deg.)90.00, 102.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rac-like GTP-binding protein ARAC6 / GTPase protein ROP5 / plant Rho protein ROP5


Mass: 19811.617 Da / Num. of mol.: 1 / Fragment: residues 1-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARAC6, RAC2, ROP5 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SBJ6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 28%(w/v) PEG 3000, 100 mM MES pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97634 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97634 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 23836 / Redundancy: 2.9 %
Reflection shellResolution: 1.53→1.6 Å / Redundancy: 1.9 %

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ROP4-GDP of model with PDB ID 2NTY

2nty


Resolution: 1.53→24.72 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26504 1191 5 %RANDOM
Rwork0.24673 ---
obs0.24765 22637 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.474 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.53→24.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 29 48 1262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221239
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9931702
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg27.9155164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73224.47438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46615182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.295153
X-RAY DIFFRACTIONr_chiral_restr0.1530.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02908
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.2552
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.2883
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.181.5811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83821299
X-RAY DIFFRACTIONr_scbond_it2.7393428
X-RAY DIFFRACTIONr_scangle_it3.9234.5402
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.531→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 76 -
Rwork0.362 1442 -
obs--100 %

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