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- PDB-2j0v: The crystal structure of Arabidopsis thaliana RAC7-ROP9: the firs... -

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Basic information

Entry
Database: PDB / ID: 2j0v
TitleThe crystal structure of Arabidopsis thaliana RAC7-ROP9: the first RAS superfamily GTPase from the plant kingdom
ComponentsRAC-LIKE GTP-BINDING PROTEIN ARAC7
KeywordsNUCLEOTIDE-BINDING PROTEIN / ROP9 / ATRAC7 / MEMBRANE / PALMITATE / RHO GTPASE / ABSCISIC ACID SIGNALING PATHWAY / DNA BINDING PROTEIN NUCLEOTIDE- BINDING / ARABIDOPSIS THALIANA / LIPOPROTEIN / GTP-BINDING / RAS SUPERFAMILY
Function / homology
Function and homology information


abscisic acid-activated signaling pathway / small GTPase-mediated signal transduction / GTPase activity / GTP binding / plasma membrane
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 ARAC7
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsSormo, C.G. / Leiros, I. / Brembu, T. / Winge, P. / Os, V. / Bones, A.M.
CitationJournal: Phytochemistry / Year: 2006
Title: The Crystal Structure of Arabidopsis Thaliana Rac7/Rop9: The First Ras Superfamily Gtpase from the Plant Kingdom.
Authors: Sormo, C.G. / Leiros, I. / Brembu, T. / Winge, P. / Os, V. / Bones, A.M.
History
DepositionAug 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAC-LIKE GTP-BINDING PROTEIN ARAC7
B: RAC-LIKE GTP-BINDING PROTEIN ARAC7
C: RAC-LIKE GTP-BINDING PROTEIN ARAC7
D: RAC-LIKE GTP-BINDING PROTEIN ARAC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,40612
Polymers93,5364
Non-polymers1,8708
Water5,332296
1
A: RAC-LIKE GTP-BINDING PROTEIN ARAC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8513
Polymers23,3841
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RAC-LIKE GTP-BINDING PROTEIN ARAC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8513
Polymers23,3841
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: RAC-LIKE GTP-BINDING PROTEIN ARAC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8513
Polymers23,3841
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: RAC-LIKE GTP-BINDING PROTEIN ARAC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8513
Polymers23,3841
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.760, 30.200, 139.360
Angle α, β, γ (deg.)90.00, 100.06, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
RAC-LIKE GTP-BINDING PROTEIN ARAC7 / GTPASE PROTEIN ROP9 / RAC7-ROP9


Mass: 23383.945 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O82480
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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


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


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTS AS A NEGATIVE REGULATOR OF ABSCISIC ACID (ABA) RESPONSES. ENGINEERED RESIDUE IN CHAIN A, ALA 3 ...ACTS AS A NEGATIVE REGULATOR OF ABSCISIC ACID (ABA) RESPONSES. ENGINEERED RESIDUE IN CHAIN A, ALA 3 TO VAL ENGINEERED RESIDUE IN CHAIN B, ALA 3 TO VAL ENGINEERED RESIDUE IN CHAIN C, ALA 3 TO VAL ENGINEERED RESIDUE IN CHAIN D, ALA 3 TO VAL
Sequence details3 AA PRIOR TO START OF MATURE SEQUENCE DUE TO THROMBIN CLEAVAGE SITE. THESE ARE GSH AND NUMBERED '- ...3 AA PRIOR TO START OF MATURE SEQUENCE DUE TO THROMBIN CLEAVAGE SITE. THESE ARE GSH AND NUMBERED '-2,-1,0'. ALSO POINT MUTATION A3V.

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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: 1.9 Å3/Da / Density % sol: 37 %
Crystal growpH: 6.5
Details: 50 MM BISTRIS PH 6.5, 10 MM MGCL2, 5 MM DTT, 200 MM KCL, 10% (W/V) PEG 2000, 10% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.78→38.18 Å / Num. obs: 61628 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.88 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MH1

1mh1


Resolution: 1.78→37.8 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.684 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3106 5 %RANDOM
Rwork0.187 ---
obs0.189 58521 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0.29 Å2
2---0.42 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.78→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5375 0 116 296 5787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225597
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9837617
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15724.455220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72315924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.11524
X-RAY DIFFRACTIONr_chiral_restr0.1190.2885
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024090
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.22442
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23853
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2311
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.2116
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.161.53588
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78925612
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.54332383
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8254.52005
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: 1.78→1.83 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 211
Rwork0.232 4240

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