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- PDB-3qle: Structural Basis for the Function of Tim50 in the Mitochondrial P... -

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Basic information

Entry
Database: PDB / ID: 3qle
TitleStructural Basis for the Function of Tim50 in the Mitochondrial Presequence Translocase
ComponentsTim50p
KeywordsCHAPERONE / Mitochondrion / preprotein translocation
Function / homology
Function and homology information


TIM23 mitochondrial import inner membrane translocase complex / protein transport / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Mitochondrial import inner membrane translocase subunit Tim50 / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Mitochondrial import inner membrane translocase subunit TIM50
Similarity search - Component
Biological speciesSaccharomyces cerevisiae EC1118 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.831 Å
AuthorsQian, X.G. / Gebert, M. / Hpker, J. / Yan, M. / Li, J.Z. / Wiedemann, N. / Laan, M.V.D. / Pfanner, N. / Sha, B.D.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural basis for the function of tim50 in the mitochondrial presequence translocase.
Authors: Qian, X. / Gebert, M. / Hopker, J. / Yan, M. / Li, J. / Wiedemann, N. / van der Laan, M. / Pfanner, N. / Sha, B.
History
DepositionFeb 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Sep 13, 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_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Tim50p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2675
Polymers23,8891
Non-polymers3774
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.109, 84.109, 116.549
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-479-

HOH

21A-489-

HOH

31A-504-

HOH

41A-529-

HOH

51A-531-

HOH

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Components

#1: Protein Tim50p


Mass: 23889.221 Da / Num. of mol.: 1 / Fragment: UNP residues 162-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae EC1118 (yeast)
Strain: Lalvin EC1118 / Prise de mousse / Gene: EC1118_1P2_2410g / Production host: Escherichia coli (E. coli) / References: UniProt: C8ZIW7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 6
Details: 100 mM MES buffer (pH 6.0), 30% (w/v) PEG4K and 0.2 M ammonium acetate, EVAPORATION, temperature 290K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 19, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. all: 21756 / Num. obs: 21756 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_351)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GHQ
Resolution: 1.831→7.989 Å / SU ML: 0.18 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 1097 5.09 %RANDOM
Rwork0.1748 ---
all0.178 21756 --
obs0.1762 21534 98.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.984 Å2 / ksol: 0.491 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1259 Å2-0 Å20 Å2
2--0.1259 Å2-0 Å2
3----0.2518 Å2
Refinement stepCycle: LAST / Resolution: 1.831→7.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 22 134 1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081556
X-RAY DIFFRACTIONf_angle_d1.1862110
X-RAY DIFFRACTIONf_dihedral_angle_d12.397588
X-RAY DIFFRACTIONf_chiral_restr0.084225
X-RAY DIFFRACTIONf_plane_restr0.005271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.831-1.91330.23071390.18332439X-RAY DIFFRACTION97
1.9133-2.01260.1941470.16522467X-RAY DIFFRACTION99
2.0126-2.13650.22641500.16522504X-RAY DIFFRACTION99
2.1365-2.29780.18061260.16072524X-RAY DIFFRACTION99
2.2978-2.52240.1991610.16242526X-RAY DIFFRACTION99
2.5224-2.87240.21821130.16872605X-RAY DIFFRACTION100
2.8724-3.56460.2111330.17932620X-RAY DIFFRACTION100
3.5646-7.98870.18061280.18442752X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 64.0328 Å / Origin y: 17.6167 Å / Origin z: 5.5753 Å
111213212223313233
T0.083 Å20.0116 Å20.0167 Å2-0.067 Å20.0038 Å2--0.0757 Å2
L0.589 °2-0.1197 °2-0.4341 °2-0.8777 °2-0.3042 °2--0.8497 °2
S0.0219 Å °0.0155 Å °0.0311 Å °0.0529 Å °0.0236 Å °0.0648 Å °0.001 Å °-0.0584 Å °0 Å °
Refinement TLS groupSelection details: (chain A and resid 13:198)

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