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- PDB-5ksy: hMiro1 C-domain GDP Complex P41212 Crystal Form -

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Basic information

Entry
Database: PDB / ID: 5ksy
TitlehMiro1 C-domain GDP Complex P41212 Crystal Form
ComponentsMitochondrial Rho GTPase 1
KeywordsHYDROLASE / Miro / GTPase / Parkin / Mitochondria
Function / homology
Function and homology information


RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / mitochondrion transport along microtubule / mitochondrion organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / Ub-specific processing proteases / GTPase activity ...RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / mitochondrion transport along microtubule / mitochondrion organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / Ub-specific processing proteases / GTPase activity / calcium ion binding / GTP binding / mitochondrion / membrane
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. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases ...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. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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 / Mitochondrial Rho GTPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.482 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 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial Rho GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6332
Polymers22,1901
Non-polymers4431
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-5 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.900, 51.900, 151.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Mitochondrial Rho GTPase 1 / hMiro-1 / Rac-GTP-binding protein-like protein / Ras homolog gene family member T1


Mass: 22189.662 Da / Num. of mol.: 1 / Fragment: C-terminal GTPase domain (UNP residues 411-592)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOT1, ARHT1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IXI2, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12 mg/mL protein, 0.1 M Tris, pH 8.5, 16% w/v PEG10000, GDP observed in the structure was carried through from the expression system during purification

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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: Jan 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.48→51.9 Å / Num. obs: 7933 / % possible obs: 100 % / Redundancy: 25.1 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 15.1
Reflection shellHighest resolution: 2.48 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLM7.1.0data reduction
Aimless0.3.8data scaling
PHENIX2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4C0L

4c0l


Resolution: 2.482→37.765 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.43
RfactorNum. reflection% reflection
Rfree0.3149 776 9.97 %
Rwork0.2659 --
obs0.2708 7786 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.482→37.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 28 8 1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021232
X-RAY DIFFRACTIONf_angle_d0.7151675
X-RAY DIFFRACTIONf_dihedral_angle_d15.497456
X-RAY DIFFRACTIONf_chiral_restr0.027189
X-RAY DIFFRACTIONf_plane_restr0.002200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4821-2.63750.37381240.30131135X-RAY DIFFRACTION99
2.6375-2.84110.45321220.33321114X-RAY DIFFRACTION97
2.8411-3.12690.38251270.3061148X-RAY DIFFRACTION100
3.1269-3.57910.34771300.28491148X-RAY DIFFRACTION98
3.5791-4.50810.25631300.23961178X-RAY DIFFRACTION99
4.5081-37.76940.29731430.25191287X-RAY DIFFRACTION100

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