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- PDB-3fp3: Crystal structure of Tom71 -

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Basic information

Entry
Database: PDB / ID: 3fp3
TitleCrystal structure of Tom71
ComponentsTPR repeat-containing protein YHR117W
KeywordsTRANSPORT PROTEIN / Tom71 / Chaperone / Mitochondria / translocation / Phosphoprotein / TPR repeat
Function / homology
Function and homology information


mitochondrion targeting sequence binding / protein import into mitochondrial matrix / protein insertion into mitochondrial inner membrane / protein targeting to mitochondrion / protein transmembrane transporter activity / mitochondrial outer membrane / mitochondrion
Similarity search - Function
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 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLi, J. / Qian, X. / Hu, J. / Sha, B.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Molecular chaperone Hsp70/Hsp90 prepares the mitochondrial outer membrane translocon receptor Tom71 for preprotein loading.
Authors: Li, J. / Qian, X. / Hu, J. / Sha, B.
History
DepositionJan 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TPR repeat-containing protein YHR117W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0018
Polymers60,5711
Non-polymers4307
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.901, 83.416, 109.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TPR repeat-containing protein YHR117W


Mass: 60571.273 Da / Num. of mol.: 1 / Fragment: UNP residues 107-639
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YHR117W / Production host: Escherichia coli (E. coli) / References: UniProt: P38825
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG4K, NaCl 0.15M, Tris 10mM, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→19.63 Å / Num. all: 47008 / Num. obs: 47008 / % possible obs: 0.99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 1.98 Å / % possible all: 0.99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GW1

2gw1


Resolution: 1.98→19.63 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.321 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.155 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22746 2508 5.1 %RANDOM
Rwork0.18698 ---
obs0.189 47008 99.87 %-
all-47008 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.554 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.98→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 19 542 4669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224253
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9755787
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3195540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83425.517203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73915756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1181516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023267
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.22287
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23061
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2450.2488
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0721.52718
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58624270
X-RAY DIFFRACTIONr_scbond_it2.69931729
X-RAY DIFFRACTIONr_scangle_it4.0294.51517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.979→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 209 -
Rwork0.215 3373 -
obs--99.53 %

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