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- PDB-6q3q: Arabidopsis OM64 TPR domain -

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Basic information

Entry
Database: PDB / ID: 6q3q
TitleArabidopsis OM64 TPR domain
Components
  • GLY-SER-LYS-MET-GLU-GLU-VAL-ASP
  • Outer envelope protein 64, mitochondrial
KeywordsPLANT PROTEIN / Tetratrico-peptide-repeat / Mitochondria / protein import / Arabodopsis thaliana
Function / homology
Function and homology information


plant-type cell wall / protein import into mitochondrial matrix / apoplast / plant-type vacuole / protein targeting to mitochondrion / chloroplast stroma / plastid / ATP-dependent protein folding chaperone / unfolded protein binding / mitochondrial outer membrane ...plant-type cell wall / protein import into mitochondrial matrix / apoplast / plant-type vacuole / protein targeting to mitochondrion / chloroplast stroma / plastid / ATP-dependent protein folding chaperone / unfolded protein binding / mitochondrial outer membrane / mRNA binding / Golgi apparatus / ATP hydrolysis activity / mitochondrion / ATP binding
Similarity search - Function
Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Outer envelope protein 64, mitochondrial / Heat shock protein 90-4
Similarity search - Component
Biological speciesArabidopsis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSchwenkert, S.
CitationJournal: Mitochondrion / Year: 2019
Title: Phosphorylation of the outer membrane mitochondrial protein OM64 influences protein import into mitochondria.
Authors: Nickel, C. / Horneff, R. / Heermann, R. / Neumann, B. / Jung, K. / Soll, J. / Schwenkert, S.
History
DepositionDec 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer envelope protein 64, mitochondrial
B: Outer envelope protein 64, mitochondrial
a: GLY-SER-LYS-MET-GLU-GLU-VAL-ASP
b: GLY-SER-LYS-MET-GLU-GLU-VAL-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,67517
Polymers29,4544
Non-polymers1,22113
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-103 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.630, 148.630, 47.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-1328-

HOH

21B-1353-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 483 - 603 / Label seq-ID: 1 - 121

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Outer envelope protein 64, mitochondrial / Mitochondrial outer membrane protein 64 / mtOM64 / Translocon at the outer membrane of chloroplasts ...Mitochondrial outer membrane protein 64 / mtOM64 / Translocon at the outer membrane of chloroplasts 64-V / AtTOC64-V


Mass: 13831.952 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis (plant) / Gene: OM64, TOC64-V, At5g09420, T5E8.220 / Production host: Escherichia coli (E. coli) / References: UniProt: F4KCL7
#2: Protein/peptide GLY-SER-LYS-MET-GLU-GLU-VAL-ASP


Mass: 894.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: O03986*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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

Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.10 M Bis-Tris pH 6.20, 0.10 M Na-Chloride, 1.10 M (NH4)2-Sulfate, 0.05 M Mg-Chloride, 0.1 M Na-Acetate, pH 4.60, 2 M (NH4)2-Sulfate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 1.54179 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 40693 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.994 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.051 / Rrim(I) all: 0.162 / Net I/σ(I): 11.7 / Num. measured all: 407295
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.119.60.6658970.8150.2250.698100
6.32-2010.20.08213310.9960.0270.08696.9

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Processing

Software
NameVersionClassification
Aimless3.3.22data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
ADDREFdata reduction
ACORNphasing
RefinementResolution: 2→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.419 / SU ML: 0.065 / SU R Cruickshank DPI: 0.0919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.095
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1682 2161 5.3 %RANDOM
Rwork0.135 ---
obs0.1367 38518 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 157.08 Å2 / Biso mean: 33.854 Å2 / Biso min: 12.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 72 681 2811
Biso mean--44.38 52.06 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192271
X-RAY DIFFRACTIONr_bond_other_d0.0020.022226
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9763050
X-RAY DIFFRACTIONr_angle_other_deg0.97135129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7545287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97824.237118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98315447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3681520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022567
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02537
Refine LS restraints NCS

Ens-ID: 1 / Number: 8528 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 191 -
Rwork0.226 2783 -
all-2974 -
obs--99.97 %

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