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- PDB-2gw1: Crystal Structure of the Yeast Tom70 -

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Basic information

Entry
Database: PDB / ID: 2gw1
TitleCrystal Structure of the Yeast Tom70
ComponentsMitochondrial precursor proteins import receptor
KeywordsPROTEIN TRANSPORT / TPR
Function / homology
Function and homology information


mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / protein import into mitochondrial matrix / protein-transporting ATPase activity / protein insertion into mitochondrial inner membrane / protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / mitochondrial outer membrane / mitochondrion
Similarity search - Function
Mitochondrial outer membrane translocase complex, subunit Tom70 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...Mitochondrial outer membrane translocase complex, subunit Tom70 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM70
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsWu, Y. / Sha, B.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Crystal structure of yeast mitochondrial outer membrane translocon member Tom70p.
Authors: Wu, Y. / Sha, B.
History
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 precursor proteins import receptor
B: Mitochondrial precursor proteins import receptor


Theoretical massNumber of molelcules
Total (without water)117,6202
Polymers117,6202
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-37 kcal/mol
Surface area46660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.880, 168.597, 82.987
Angle α, β, γ (deg.)90.00, 102.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitochondrial precursor proteins import receptor / 70 kDa mitochondrial outer membrane protein / Translocase of outer membrane TOM70


Mass: 58810.211 Da / Num. of mol.: 2 / Fragment: cytosolic fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TOM70, MAS70, OMP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07213
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG 4000, 0.1M ammonium citrate, 0.2M ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2006
RadiationMonochromator: 0.97903 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 25274 / % possible obs: 95 %
Reflection shellResolution: 3→3.12 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3→46.17 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 946224.81 / Data cutoff high rms absF: 946224.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1128 4.8 %RANDOM
Rwork0.2585 ---
all0.2585 ---
obs0.2585 23334 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.3333 Å2 / ksol: 0.318691 e/Å3
Displacement parametersBiso mean: 79.9 Å2
Baniso -1Baniso -2Baniso -3
1-11.4 Å20 Å29.14 Å2
2---17.01 Å20 Å2
3---5.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7858 0 0 126 7984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.456 187 5.1 %
Rwork0.42 3448 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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