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- PDB-5ksz: hMiro EF hand and cGTPase domains in the GMPPCP-bound state -

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Basic information

Entry
Database: PDB / ID: 5ksz
TitlehMiro EF hand and cGTPase domains in the GMPPCP-bound state
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. / EF-hand / Recoverin; domain 1 ...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. / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Mitochondrial Rho GTPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.1Oct 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)49,6715
Polymers49,0661
Non-polymers6054
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-15 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.180, 74.180, 218.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 49065.859 Da / Num. of mol.: 1 / Fragment: hand and cGTPase domains (UNP residues 177-592)
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.07 Å3/Da / Density % sol: 59.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 12 mg/mL protein, 6 mM magnesium chloride, 10 mM GMPPCP, 0.2 M ammonium sulfate, 0.1 M trisodium citrate, pH 5.6, 17.5% w/v PEG4000

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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: Apr 19, 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: 2.5→25 Å / Num. obs: 22095 / % possible obs: 100 % / Redundancy: 17.8 % / Rmerge(I) obs: 0.249 / Net I/σ(I): 10.1
Reflection shellHighest resolution: 2.5 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHENIX2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4C0L

4c0l


Resolution: 2.5→24.68 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 35.04
RfactorNum. reflection% reflection
Rfree0.2657 1998 4.97 %
Rwork0.2106 --
obs0.2134 20057 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 35 30 3276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043339
X-RAY DIFFRACTIONf_angle_d0.6124523
X-RAY DIFFRACTIONf_dihedral_angle_d11.5911229
X-RAY DIFFRACTIONf_chiral_restr0.024506
X-RAY DIFFRACTIONf_plane_restr0.003573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.38581260.33842759X-RAY DIFFRACTION99
2.5625-2.63170.44581260.33352747X-RAY DIFFRACTION100
2.6317-2.7090.4221350.32362694X-RAY DIFFRACTION100
2.709-2.79640.37221690.32172689X-RAY DIFFRACTION100
2.7964-2.89620.42691540.32322725X-RAY DIFFRACTION99
2.8962-3.01190.38991440.31282740X-RAY DIFFRACTION100
3.0119-3.14870.35781590.28522715X-RAY DIFFRACTION100
3.1487-3.31440.27531500.24992715X-RAY DIFFRACTION100
3.3144-3.52150.30641230.23052778X-RAY DIFFRACTION100
3.5215-3.79250.25461410.20122712X-RAY DIFFRACTION100
3.7925-4.17250.22041660.16282713X-RAY DIFFRACTION100
4.1725-4.77250.19551450.15212739X-RAY DIFFRACTION100
4.7725-5.99850.23151230.17092751X-RAY DIFFRACTION100
5.9985-24.68130.19191370.15942755X-RAY DIFFRACTION100

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