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- PDB-4u5x: Structure of plant small GTPase OsRac1 complexed with the non-hyd... -

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Basic information

Entry
Database: PDB / ID: 4u5x
TitleStructure of plant small GTPase OsRac1 complexed with the non-hydrolyzable GTP analog GMPPNP
ComponentsRac-like GTP-binding protein 1
KeywordsGTP-BINDING PROTEIN / Small GTPase / Rac / Plant
Function / homology
Function and homology information


cortical cytoskeleton organization / small GTPase-mediated signal transduction / cell projection / actin filament organization / regulation of actin cytoskeleton organization / defense response / cell cortex / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization ...cortical cytoskeleton organization / small GTPase-mediated signal transduction / cell projection / actin filament organization / regulation of actin cytoskeleton organization / defense response / cell cortex / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization / cytoskeleton / intracellular membrane-bounded organelle / GTPase activity / GTP binding / protein kinase binding / enzyme binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Small GTPase Rho / small GTPase Rho family profile. / 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 / Rac-like GTP-binding protein 1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOhki, I. / Kosami, K. / Fujiwara, T. / Nakagawa, A. / Shimamoto, K. / Kojima, C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Crystal Structure of the Plant Small GTPase OsRac1 Reveals Its Mode of Binding to NADPH Oxidase
Authors: Kosami, K. / Ohki, I. / Nagano, M. / Furuita, K. / Sugiki, T. / Kawano, Y. / Kawasaki, T. / Fujiwara, T. / Nakagawa, A. / Shimamoto, K. / Kojima, C.
History
DepositionJul 25, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 8, 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 / refine_hist / struct_conn
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 / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rac-like GTP-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5106
Polymers19,6881
Non-polymers8235
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-15 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.755, 59.087, 64.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rac-like GTP-binding protein 1 / OsRac1


Mass: 19687.576 Da / Num. of mol.: 1 / Fragment: UNP residues 8-183 / Mutation: C32S, Q68L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: RAC1, Os01g0229400, LOC_Os01g12900 / Plasmid: pGEX-6P3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9SSX0
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 6000, MES buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 11521 / % possible obs: 99.8 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 7.7 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J0V

2j0v


Resolution: 1.9→43.54 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.257 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 550 4.8 %RANDOM
Rwork0.15651 ---
obs0.15872 10901 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.078 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2---0.66 Å20 Å2
3----1.21 Å2
Refinement stepCycle: 1 / Resolution: 1.9→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 51 90 1525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021459
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2022.0051982
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.50823.10358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26215241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4141511
X-RAY DIFFRACTIONr_chiral_restr0.1440.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211061
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 28 -
Rwork0.173 683 -
obs--96.87 %

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