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- PDB-5kut: hMiro2 C-terminal GTPase domain, GDP-bound -

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Basic information

Entry
Database: PDB / ID: 5kut
TitlehMiro2 C-terminal GTPase domain, GDP-bound
ComponentsMitochondrial Rho GTPase 2
KeywordsHYDROLASE / Miro / GTPase / Parkin / Mitochondria
Function / homology
Function and homology information


: / : / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / regulation of small GTPase mediated signal transduction / mitochondrion transport along microtubule / mitochondrion organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane ...: / : / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / regulation of small GTPase mediated signal transduction / mitochondrion transport along microtubule / mitochondrion organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / GTPase activity / calcium ion binding / GTP binding / mitochondrion / membrane / cytosol
Similarity search - Function
Mitochondrial Rho GTPase 1/3, EF hand associated, type-1 / EF hand associated, type-2 / MIRO domain / Mitochondrial Rho GTPase / EF hand associated / EF hand associated / Miro domain profile. / Small GTPase / Ras family / EF-Hand 1, calcium-binding site ...Mitochondrial Rho GTPase 1/3, EF hand associated, type-1 / EF hand associated, type-2 / MIRO domain / Mitochondrial Rho GTPase / EF hand associated / EF hand associated / Miro domain profile. / Small GTPase / Ras family / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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 / Mitochondrial Rho GTPase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.693 Å
AuthorsKlosowiak, J.L. / Focia, P.J. / Rice, S.E. / Freymann, D.M.
CitationJournal: Sci Rep / Year: 2016
Title: Structural insights into Parkin substrate lysine targeting from minimal Miro substrates.
Authors: Klosowiak, J.L. / Park, S. / Smith, K.P. / French, M.E. / Focia, P.J. / Freymann, D.M. / Rice, S.E.
History
DepositionJul 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial Rho GTPase 2
B: Mitochondrial Rho GTPase 2
C: Mitochondrial Rho GTPase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1719
Polymers60,7683
Non-polymers1,4036
Water6,828379
1
A: Mitochondrial Rho GTPase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7243
Polymers20,2561
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitochondrial Rho GTPase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7243
Polymers20,2561
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mitochondrial Rho GTPase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7243
Polymers20,2561
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.610, 122.760, 103.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-833-

HOH

21C-784-

HOH

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Components

#1: Protein Mitochondrial Rho GTPase 2 / hMiro-2 / Ras homolog gene family member T2


Mass: 20256.082 Da / Num. of mol.: 3 / Fragment: C-terminal GTPase domain (UNP residues 409-588)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOT2, ARHT2, C16orf39 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IXI1, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 14 mg/mL protein, 0.2 M magnesium formate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 26, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.69→52.8 Å / Num. obs: 57061 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.1
Reflection shellHighest resolution: 1.69 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4C0L

4c0l


Resolution: 1.693→37.576 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 27.93
RfactorNum. reflection% reflection
Rfree0.2385 2804 4.96 %
Rwork0.2179 --
obs0.219 56761 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.693→37.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 0 87 379 4235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054081
X-RAY DIFFRACTIONf_angle_d0.645590
X-RAY DIFFRACTIONf_dihedral_angle_d11.6772467
X-RAY DIFFRACTIONf_chiral_restr0.044624
X-RAY DIFFRACTIONf_plane_restr0.005721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.693-1.71230.37451670.37643474X-RAY DIFFRACTION97
1.7123-1.73240.36672040.34743385X-RAY DIFFRACTION99
1.7324-1.75350.31812100.33993445X-RAY DIFFRACTION98
1.7535-1.77570.31891940.32693412X-RAY DIFFRACTION99
1.7757-1.79910.37141910.32833469X-RAY DIFFRACTION98
1.7991-1.82370.30431800.31663439X-RAY DIFFRACTION98
1.8237-1.84980.28361510.30633509X-RAY DIFFRACTION99
1.8498-1.87740.3391700.32313500X-RAY DIFFRACTION99
1.8774-1.90670.42151750.41743317X-RAY DIFFRACTION95
1.9067-1.9380.50281690.46613383X-RAY DIFFRACTION96
1.938-1.97140.37791490.31833471X-RAY DIFFRACTION99
1.9714-2.00730.26121840.2713461X-RAY DIFFRACTION99
2.0073-2.04590.27641520.25223570X-RAY DIFFRACTION99
2.0459-2.08760.26011750.24073512X-RAY DIFFRACTION100
2.0876-2.1330.26552060.24423431X-RAY DIFFRACTION99
2.133-2.18260.32291820.26023474X-RAY DIFFRACTION100
2.1826-2.23720.36951880.31873349X-RAY DIFFRACTION95
2.2372-2.29770.39391910.35173384X-RAY DIFFRACTION96
2.2977-2.36530.29081890.22973507X-RAY DIFFRACTION100
2.3653-2.44160.22362200.21663462X-RAY DIFFRACTION100
2.4416-2.52890.20471770.213518X-RAY DIFFRACTION100
2.5289-2.63010.23361610.21223528X-RAY DIFFRACTION100
2.6301-2.74970.24631920.2043477X-RAY DIFFRACTION100
2.7497-2.89470.21241830.20393548X-RAY DIFFRACTION100
2.8947-3.0760.2251750.21173498X-RAY DIFFRACTION100
3.076-3.31330.20831710.18943517X-RAY DIFFRACTION100
3.3133-3.64650.21381710.1793549X-RAY DIFFRACTION100
3.6465-4.17360.20641540.16493506X-RAY DIFFRACTION100
4.1736-5.2560.17832070.15023515X-RAY DIFFRACTION100
5.256-37.58540.15461930.1653441X-RAY DIFFRACTION98

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