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- PDB-2cw9: Crystal structure of human Tim44 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2cw9
TitleCrystal structure of human Tim44 C-terminal domain
Componentstranslocase of inner mitochondrial membrane
KeywordsPROTEIN TRANSPORT / Structure Genomics / TIM / Structural Genomics / NPPFSA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / Mitochondrial protein import / protein targeting to mitochondrion / intracellular protein transport / fibrillar center / protein-folding chaperone binding / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / ATP binding
Similarity search - Function
Nuclear Transport Factor 2; Chain: A, - #240 / Mitochondrial import inner membrane translocase subunit Tim44 / Tim44-like / Tim44-like domain / Tim44-like domain / Tim44 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Mitochondrial import inner membrane translocase subunit TIM44
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHanda, N. / Kishishita, S. / Morita, S. / Kinoshita, Y. / Nagano, Y. / Uda, H. / Terada, T. / Uchikubo, T. / Takemoto, C. / Jin, Z. ...Handa, N. / Kishishita, S. / Morita, S. / Kinoshita, Y. / Nagano, Y. / Uda, H. / Terada, T. / Uchikubo, T. / Takemoto, C. / Jin, Z. / Chrzas, J. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of the human Tim44 C-terminal domain in complex with pentaethylene glycol: ligand-bound form.
Authors: Handa, N. / Kishishita, S. / Morita, S. / Akasaka, R. / Jin, Z. / Chrzas, J. / Chen, L. / Liu, Z.J. / Wang, B.C. / Sugano, S. / Tanaka, A. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_leaving_atom_flag / _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: translocase of inner mitochondrial membrane
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4123
Polymers21,9351
Non-polymers4772
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.119, 108.119, 114.056
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1-

HOH

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Components

#1: Protein translocase of inner mitochondrial membrane


Mass: 21935.025 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell free / References: UniProt: O43615
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG400, HEPES, ammonium sulfate, glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 23, 2005 / Details: mirrors
RadiationMonochromator: Si / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 31350 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 20.5 Å2 / Rsym value: 0.065 / Net I/σ(I): 25.6
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 0.313 / % possible all: 95.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2021435.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1553 5 %RANDOM
Rwork0.218 ---
obs0.218 31278 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.4 Å2 / ksol: 0.364381 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.25 Å20 Å2
2---0.45 Å20 Å2
3---0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 32 151 1624
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.812.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 244 4.9 %
Rwork0.263 4729 -
obs-244 96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION31pe.param1pe.top

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