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- PDB-2ciu: Structure of the IMS domain of the mitochondrial import protein T... -

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Basic information

Entry
Database: PDB / ID: 2ciu
TitleStructure of the IMS domain of the mitochondrial import protein Tim21 from S. cerevisiae
ComponentsIMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM21 MITOCHONDRIAL
KeywordsPROTEIN TRANSPORT / MITOCHONDRIAL IMPORT / INNER MEMBRANE / MEMBRANE / MITOCHONDRION / TRANSIT PEPTIDE / TRANSLOCATION / TRANSMEMBRANE / TRANSPORT
Function / homology
Function and homology information


TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / protein insertion into mitochondrial inner membrane / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Mitochondrial import inner membrane translocase subunit Tim21 / Mitochondrial import inner membrane translocase subunit Tim21 / Tim21 IMS domain superfamily / TIM21 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Mitochondrial import inner membrane translocase subunit TIM21
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsAlbrecht, R. / Zeth, K. / Rehling, P. / Pfanner, N.
CitationJournal: Embo Rep. / Year: 2006
Title: The Tim21 Binding Domain Connects the Preprotein Translocases of Both Mitochondrial Membranes
Authors: Albrecht, R. / Rehling, P. / Chacinska, A. / Brix, J. / Cadamuro, S.A. / Volkmer, R. / Guiard, B. / Pfanner, N. / Zeth, K.
History
DepositionMar 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM21 MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)14,7631
Polymers14,7631
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.310, 58.820, 62.550
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 IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM21 MITOCHONDRIAL / TIM21P


Mass: 14763.003 Da / Num. of mol.: 1 / Fragment: IMS DOMAIN, RESIDUES 103-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Organ: MITOCHONDRIUM / Plasmid: PPROEXHTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53220
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Compound detailsESSENTIAL COMPONENT OF THE TIM23 COMPLEX, A COMPLEX THAT MEDIATES THE TRANSLOCATION OF TRANSIT ...ESSENTIAL COMPONENT OF THE TIM23 COMPLEX, A COMPLEX THAT MEDIATES THE TRANSLOCATION OF TRANSIT PEPTIDE-CONTAINING PROTEINS ACROSS THE MITOCHONDRIAL INNER MEMBRANE

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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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growpH: 6 / Details: 0.2 M LI2SO4, 0.1 M BIS-TRIS PH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 16515 / % possible obs: 97.5 % / Observed criterion σ(I): 3.72 / Redundancy: 3.33 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18
Reflection shellResolution: 1.58→1.68 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.72 / % possible all: 94

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 909332.09 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 803 4.9 %RANDOM
Rwork0.1975 ---
obs0.1975 16047 98.3 %-
Solvent computationBsol: 68.9141 Å2 / ksol: 0.419383 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.929 Å20 Å20 Å2
2--3.05 Å20 Å2
3----1.122 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 0 167 1170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 130 5 %
Rwork0.228 2475 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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