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- PDB-4qqf: Crystal structure of mitochondrial import inner membrane transloc... -

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Basic information

Entry
Database: PDB / ID: 4qqf
TitleCrystal structure of mitochondrial import inner membrane translocase subunit TIM50
ComponentsMitochondrial import inner membrane translocase subunit TIM50
KeywordsTRANSPORT PROTEIN / single domain / protein import / mitochondrial
Function / homology
Function and homology information


mitochondrion targeting sequence binding / TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / regulation of mitochondrial membrane permeability / phosphoprotein phosphatase activity / mitochondrial inner membrane / membrane => GO:0016020 / mitochondrion / identical protein 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
Mitochondrial import inner membrane translocase subunit TIM50
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.672 Å
AuthorsLi, J.Z.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: The structure of Tim50(164-361) suggests the mechanism by which Tim50 receives mitochondrial presequences.
Authors: Li, J. / Sha, B.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 20, 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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
D: Mitochondrial import inner membrane translocase subunit TIM50
A: Mitochondrial import inner membrane translocase subunit TIM50
B: Mitochondrial import inner membrane translocase subunit TIM50
C: Mitochondrial import inner membrane translocase subunit TIM50
E: Mitochondrial import inner membrane translocase subunit TIM50
F: Mitochondrial import inner membrane translocase subunit TIM50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,53212
Polymers142,3866
Non-polymers1466
Water88349
1
D: Mitochondrial import inner membrane translocase subunit TIM50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7552
Polymers23,7311
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mitochondrial import inner membrane translocase subunit TIM50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7552
Polymers23,7311
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Mitochondrial import inner membrane translocase subunit TIM50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7552
Polymers23,7311
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Mitochondrial import inner membrane translocase subunit TIM50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7552
Polymers23,7311
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Mitochondrial import inner membrane translocase subunit TIM50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7552
Polymers23,7311
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Mitochondrial import inner membrane translocase subunit TIM50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7552
Polymers23,7311
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.287, 164.287, 150.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Mitochondrial import inner membrane translocase subunit TIM50


Mass: 23731.064 Da / Num. of mol.: 6 / Fragment: UNP residues 164-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TIM50, YPL063W / Production host: Escherichia coli (E. coli) / References: UniProt: Q02776
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.57 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0 M magnesium sulfate, 100 mM Tris, pH 7.5, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Jun 6, 2014
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.672→116.168 Å / Num. all: 58798 / Num. obs: 58660 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.076 / Rsym value: 0.071 / Net I/σ(I): 42.2
Reflection shellResolution: 2.672→2.77 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.714 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QLE

3qle


Resolution: 2.672→38.519 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 27.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 2934 5.01 %
Rwork0.212 --
obs0.2139 58620 99.75 %
all-58624 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.672→38.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9377 0 6 49 9432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119594
X-RAY DIFFRACTIONf_angle_d1.58413066
X-RAY DIFFRACTIONf_dihedral_angle_d13.9933625
X-RAY DIFFRACTIONf_chiral_restr0.0671377
X-RAY DIFFRACTIONf_plane_restr0.011691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6724-2.71620.37921370.29672591X-RAY DIFFRACTION98
2.7162-2.7630.30491370.28752604X-RAY DIFFRACTION100
2.763-2.81320.30561380.28732611X-RAY DIFFRACTION100
2.8132-2.86730.36421380.28912615X-RAY DIFFRACTION100
2.8673-2.92580.35831380.29762622X-RAY DIFFRACTION100
2.9258-2.98940.34351380.28262634X-RAY DIFFRACTION100
2.9894-3.0590.30411390.28242634X-RAY DIFFRACTION100
3.059-3.13540.35061380.27142609X-RAY DIFFRACTION100
3.1354-3.22020.32451380.26032634X-RAY DIFFRACTION100
3.2202-3.31490.29091380.25242619X-RAY DIFFRACTION100
3.3149-3.42180.27691410.24082668X-RAY DIFFRACTION100
3.4218-3.5440.31370.22722619X-RAY DIFFRACTION100
3.544-3.68580.28121400.21632642X-RAY DIFFRACTION100
3.6858-3.85340.26021390.20922660X-RAY DIFFRACTION100
3.8534-4.05630.21761400.19642650X-RAY DIFFRACTION100
4.0563-4.31020.21781400.18342665X-RAY DIFFRACTION100
4.3102-4.64250.21441400.16722667X-RAY DIFFRACTION100
4.6425-5.10870.20351410.16432688X-RAY DIFFRACTION100
5.1087-5.84570.21491430.18692709X-RAY DIFFRACTION100
5.8457-7.35660.24661450.21712738X-RAY DIFFRACTION100
7.3566-38.52290.22811490.20252807X-RAY DIFFRACTION97

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