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- PDB-4bm5: Chloroplast inner membrane protein TIC110 -

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Basic information

Entry
Database: PDB / ID: 4bm5
TitleChloroplast inner membrane protein TIC110
ComponentsSIMILAR TO CHLOROPLAST INNER MEMBRANE PROTEIN TIC110
KeywordsPROTEIN TRANSPORT
Function / homologyProtein TIC110, chloroplastic / Chloroplast envelope transporter / TOC-TIC supercomplex I / protein import into chloroplast stroma / membrane / Similar to chloroplast inner membrane protein Tic110
Function and homology information
Biological speciesCYANIDIOSCHYZON MEROLAE (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 4.2 Å
AuthorsTsai, J.-Y. / Chu, C.-C. / Yeh, Y.-H. / Chen, L.-J. / Li, H.-m. / Hsiao, C.-D.
CitationJournal: Plant J. / Year: 2013
Title: Structural Characterizations of Chloroplast Translocon Protein Tic110.
Authors: Tsai, J.-Y. / Chu, C.-C. / Yeh, Y.-H. / Chen, L.-J. / Li, H.-M. / Hsiao, C.-D.
History
DepositionMay 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2May 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIMILAR TO CHLOROPLAST INNER MEMBRANE PROTEIN TIC110


Theoretical massNumber of molelcules
Total (without water)39,4711
Polymers39,4711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.100, 121.100, 242.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein SIMILAR TO CHLOROPLAST INNER MEMBRANE PROTEIN TIC110 / CMC


Mass: 39470.633 Da / Num. of mol.: 1 / Fragment: RESIDUES 871-1218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CYANIDIOSCHYZON MEROLAE (eukaryote) / Strain: 10D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M1V6H9

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.5 Å3/Da / Density % sol: 81.08 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9787
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 4.2→30 Å / Num. obs: 8171 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 27.8

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Processing

Software
NameVersionClassification
CNS1.3refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 4.2→27.37 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 185959.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.366 706 10.6 %RANDOM
Rwork0.35 ---
obs0.35 6673 81.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 1339.51 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 74.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å20 Å20 Å2
2--3.63 Å20 Å2
3----7.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error1 Å0.82 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.8 Å
Refinement stepCycle: LAST / Resolution: 4.2→27.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 0 0 1350
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg2.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it23.761.5
X-RAY DIFFRACTIONc_mcangle_it36.972
X-RAY DIFFRACTIONc_scbond_it59.362
X-RAY DIFFRACTIONc_scangle_it61.832.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 4.2→4.46 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.432 90 10.2 %
Rwork0.379 793 -
obs--66.8 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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