[English] 日本語
Yorodumi
- PDB-6hpg: Arabidopsis OM64 TPR domain -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more