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- PDB-6hpg: Arabidopsis OM64 TPR domain -

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Basic information

Entry
Database: PDB / ID: 6hpg
TitleArabidopsis OM64 TPR domain
Components
  • Heat shock protein 90-4
  • 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 / protein targeting to mitochondrion / plant-type vacuole / plastid / chloroplast stroma / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding ...plant-type cell wall / protein import into mitochondrial matrix / apoplast / protein targeting to mitochondrion / plant-type vacuole / plastid / chloroplast stroma / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / mitochondrial outer membrane / protein stabilization / mRNA binding / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / plasma membrane / cytosol
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 / TPR repeat region circular profile. ...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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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 thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
DepositionSep 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 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.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer envelope protein 64, mitochondrial
B: Outer envelope protein 64, mitochondrial
C: Outer envelope protein 64, mitochondrial
D: Outer envelope protein 64, mitochondrial
E: Outer envelope protein 64, mitochondrial
F: Outer envelope protein 64, mitochondrial
a: Heat shock protein 90-4
b: Heat shock protein 90-4
c: Heat shock protein 90-4
d: Heat shock protein 90-4
e: Heat shock protein 90-4
f: Heat shock protein 90-4


Theoretical massNumber of molelcules
Total (without water)88,10912
Polymers88,10912
Non-polymers00
Water10,971609
1
A: Outer envelope protein 64, mitochondrial
a: Heat shock protein 90-4


Theoretical massNumber of molelcules
Total (without water)14,6852
Polymers14,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-4 kcal/mol
Surface area7120 Å2
MethodPISA
2
B: Outer envelope protein 64, mitochondrial
b: Heat shock protein 90-4


Theoretical massNumber of molelcules
Total (without water)14,6852
Polymers14,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-4 kcal/mol
Surface area6950 Å2
MethodPISA
3
C: Outer envelope protein 64, mitochondrial
c: Heat shock protein 90-4


Theoretical massNumber of molelcules
Total (without water)14,6852
Polymers14,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-3 kcal/mol
Surface area6940 Å2
MethodPISA
4
D: Outer envelope protein 64, mitochondrial
d: Heat shock protein 90-4


Theoretical massNumber of molelcules
Total (without water)14,6852
Polymers14,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-4 kcal/mol
Surface area7110 Å2
MethodPISA
5
E: Outer envelope protein 64, mitochondrial
e: Heat shock protein 90-4


Theoretical massNumber of molelcules
Total (without water)14,6852
Polymers14,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-4 kcal/mol
Surface area6940 Å2
MethodPISA
6
F: Outer envelope protein 64, mitochondrial
f: Heat shock protein 90-4


Theoretical massNumber of molelcules
Total (without water)14,6852
Polymers14,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-3 kcal/mol
Surface area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.388, 61.135, 106.563
Angle α, β, γ (deg.)87.570, 87.990, 78.260
Int Tables number1
Space group name H-MP1

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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: 13789.916 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: OM64, TOC64-V, At5g09420, T5E8.220 / Production host: Escherichia coli (E. coli) / References: UniProt: F4KCL7
#2: Protein/peptide
Heat shock protein 90-4 / AtHsp90-4 / Heat shock protein 81-4 / Hsp81-4


Mass: 894.967 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HSP90-4, HSP81-4, At5g56000, MDA7.4 / Production host: Escherichia coli (E. coli) / References: UniProt: O03986
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric acid, pH 3.5, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 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: 0.966 Å / Relative weight: 1
ReflectionResolution: 2→29.91 Å / Num. obs: 45460 / % possible obs: 92.7 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.068 / Rrim(I) all: 0.097 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
2-2.111.70.45464510.4540.64289.3
6.32-29.071.80.02713920.0270.03889.6

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
ADDREFdata reduction
ACORNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VYI

2vyi


Resolution: 2→29.91 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.886 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.217
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 2395 5.3 %RANDOM
Rwork0.1821 ---
obs0.1864 43064 92.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.59 Å2 / Biso mean: 32.094 Å2 / Biso min: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.64 Å20.69 Å20.01 Å2
2---2.64 Å2-0.9 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 2→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 0 609 6597
Biso mean---36.3 -
Num. residues----755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196078
X-RAY DIFFRACTIONr_bond_other_d0.0020.025963
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9548122
X-RAY DIFFRACTIONr_angle_other_deg0.963313687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5135746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16124.6300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.572151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0121544
X-RAY DIFFRACTIONr_chiral_restr0.0830.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021417
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 187 -
Rwork0.333 3026 -
all-3213 -
obs--88.63 %

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