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- PDB-5ksp: hMiro1 C-domain GDP Complex C2221 Crystal Form -

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Basic information

Entry
Database: PDB / ID: 5ksp
TitlehMiro1 C-domain GDP Complex C2221 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: 2.162 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 8, 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
B: Mitochondrial Rho GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9606
Polymers44,0032
Non-polymers9574
Water5,260292
1
A: Mitochondrial Rho GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4803
Polymers22,0011
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitochondrial Rho GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4803
Polymers22,0011
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.070, 72.640, 151.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 22001.414 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 40.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15 mg/mL protein, 6 mM magnesium chloride, 0.1 M Tris, pH 8.5, 12% w/v PEG4000, 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: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.16→75.9 Å / Num. obs: 19991 / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 14.8
Reflection shellHighest resolution: 2.16 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: 2.162→48.877 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.54 / Phase error: 23.65
RfactorNum. reflection% reflection
Rfree0.2412 1951 5.17 %
Rwork0.1929 --
obs0.1954 19951 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.162→48.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 58 292 2863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032625
X-RAY DIFFRACTIONf_angle_d0.6163556
X-RAY DIFFRACTIONf_dihedral_angle_d13.958984
X-RAY DIFFRACTIONf_chiral_restr0.025398
X-RAY DIFFRACTIONf_plane_restr0.003440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1622-2.21630.28861530.27532551X-RAY DIFFRACTION100
2.2163-2.27620.30471200.25632605X-RAY DIFFRACTION100
2.2762-2.34320.27661640.22932575X-RAY DIFFRACTION100
2.3432-2.41880.29031160.2212526X-RAY DIFFRACTION100
2.4188-2.50530.31481320.21612552X-RAY DIFFRACTION100
2.5053-2.60560.29891330.22172581X-RAY DIFFRACTION100
2.6056-2.72410.2851290.21872578X-RAY DIFFRACTION100
2.7241-2.86770.24211690.21282506X-RAY DIFFRACTION100
2.8677-3.04740.27941560.21252536X-RAY DIFFRACTION100
3.0474-3.28260.23971580.1932569X-RAY DIFFRACTION100
3.2826-3.61290.23861350.17072536X-RAY DIFFRACTION100
3.6129-4.13540.16251510.15292550X-RAY DIFFRACTION100
4.1354-5.20930.17381260.15022554X-RAY DIFFRACTION100
5.2093-48.8890.2861090.19042593X-RAY DIFFRACTION100

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