[English] 日本語
Yorodumi
- PDB-7c62: The Crystal Structure of Parkinson disease protein 7 (DJ-1) from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c62
TitleThe Crystal Structure of Parkinson disease protein 7 (DJ-1) from Biortus
ComponentsProtein/nucleic acid deglycase DJ-1
KeywordsCHAPERONE / oxidative stress sensor / redox-sensitive chaperone / protease
Function / homology
Function and homology information


tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / glutathione deglycation / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate ...tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / glutathione deglycation / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly / negative regulation of TRAIL-activated apoptotic signaling pathway / positive regulation of pyrroline-5-carboxylate reductase activity / positive regulation of tyrosine 3-monooxygenase activity / positive regulation of L-dopa biosynthetic process / positive regulation of L-dopa decarboxylase activity / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of ubiquitin-specific protease activity / protein deglycation, glyoxal removal / glycolate biosynthetic process / guanine deglycation, glyoxal removal / glyoxal metabolic process / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / guanine deglycation / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / oxidoreductase activity, acting on peroxide as acceptor / protein deglycase activity / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of dopamine biosynthetic process / superoxide dismutase copper chaperone activity / positive regulation of NAD(P)H oxidase activity / positive regulation of autophagy of mitochondrion / lactate biosynthetic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular detoxification of aldehyde / positive regulation of superoxide dismutase activity / small protein activating enzyme binding / Hydrolases; Acting on ester bonds; Thioester hydrolases / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of ubiquitin-protein transferase activity / peroxiredoxin activity / detoxification of copper ion / negative regulation of protein acetylation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of transcription regulatory region DNA binding / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of androgen receptor activity / membrane hyperpolarization / protein deglycosylation / negative regulation of protein sumoylation / oxygen sensor activity / regulation of androgen receptor signaling pathway / negative regulation of protein export from nucleus / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cupric ion binding / ubiquitin-like protein conjugating enzyme binding / insulin secretion / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / dopamine uptake involved in synaptic transmission / positive regulation of reactive oxygen species biosynthetic process / nuclear androgen receptor binding / hydrogen peroxide metabolic process / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / single fertilization / membrane depolarization / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / negative regulation of protein ubiquitination / activation of protein kinase B activity / mitochondrion organization / adult locomotory behavior / SUMOylation of transcription cofactors / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein-containing complex assembly / adherens junction / Late endosomal microautophagy / negative regulation of protein kinase activity / mitochondrial intermembrane space / PML body / cellular response to hydrogen peroxide / autophagy
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.027 Å
AuthorsWang, F. / Lin, D. / Lv, Z. / Tan, J.
CitationJournal: To Be Published
Title: The Crystal Structure of Parkinson disease protein 7 (DJ-1) from Biortus.
Authors: Wang, F. / Lin, D. / Lv, Z. / Tan, J.
History
DepositionMay 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Structure summary / Category: citation / database_2 / struct
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein/nucleic acid deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0222
Polymers21,9301
Non-polymers921
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint0 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.570, 74.570, 74.956
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Protein/nucleic acid deglycase DJ-1 / Maillard deglycase / Oncogene DJ1 / Parkinson disease protein 7 / Parkinsonism-associated deglycase ...Maillard deglycase / Oncogene DJ1 / Parkinson disease protein 7 / Parkinsonism-associated deglycase / Protein DJ-1 / DJ-1


Mass: 21930.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99497, Hydrolases; Acting on ester bonds; Thioester hydrolases, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, protein deglycase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.1 M DL-Malic acid pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.027→50 Å / Num. obs: 16019 / % possible obs: 99.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.1
Reflection shellResolution: 2.03→2.07 Å / Rmerge(I) obs: 0.506 / Num. unique obs: 786

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1pdv

1pdv


Resolution: 2.027→26.446 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.152 / SU B: 2.51 / SU ML: 0.069 / Average fsc free: 0.961 / Average fsc work: 0.9667 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1736 847 5.292 %
Rwork0.152 15158 -
all0.153 --
obs-16005 99.732 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.223 Å2
Baniso -1Baniso -2Baniso -3
1-0.486 Å20.243 Å20 Å2
2--0.486 Å2-0 Å2
3----1.577 Å2
Refinement stepCycle: LAST / Resolution: 2.027→26.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 6 151 1532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131412
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171408
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.6361909
X-RAY DIFFRACTIONr_angle_other_deg1.1951.5793274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38123.50957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93415256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.732157
X-RAY DIFFRACTIONr_chiral_restr0.0520.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021573
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
X-RAY DIFFRACTIONr_nbd_refined0.1850.2269
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.21235
X-RAY DIFFRACTIONr_nbtor_refined0.140.2671
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2112
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.216
X-RAY DIFFRACTIONr_nbd_other0.1980.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.214
X-RAY DIFFRACTIONr_mcbond_it0.9492.72754
X-RAY DIFFRACTIONr_mcbond_other0.942.718753
X-RAY DIFFRACTIONr_mcangle_it1.5614.074943
X-RAY DIFFRACTIONr_mcangle_other1.564.077944
X-RAY DIFFRACTIONr_scbond_it1.4322.962658
X-RAY DIFFRACTIONr_scbond_other1.4312.965659
X-RAY DIFFRACTIONr_scangle_it2.3544.334965
X-RAY DIFFRACTIONr_scangle_other2.3534.337966
X-RAY DIFFRACTIONr_lrange_it4.18533.8411532
X-RAY DIFFRACTIONr_lrange_other4.00333.3181507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.027-2.080.232600.2041093X-RAY DIFFRACTION98.295
2.08-2.1370.167650.1811066X-RAY DIFFRACTION100
2.137-2.1990.206460.1671082X-RAY DIFFRACTION100
2.199-2.2660.156650.16993X-RAY DIFFRACTION100
2.266-2.340.184490.155994X-RAY DIFFRACTION100
2.34-2.4220.227520.156957X-RAY DIFFRACTION100
2.422-2.5140.169550.162921X-RAY DIFFRACTION100
2.514-2.6160.182570.163880X-RAY DIFFRACTION100
2.616-2.7320.177510.157857X-RAY DIFFRACTION100
2.732-2.8650.192400.159830X-RAY DIFFRACTION100
2.865-3.020.202360.153794X-RAY DIFFRACTION100
3.02-3.2030.184280.152758X-RAY DIFFRACTION100
3.203-3.4230.17400.145696X-RAY DIFFRACTION99.8643
3.423-3.6970.15530.131639X-RAY DIFFRACTION100
3.697-4.0480.128370.122603X-RAY DIFFRACTION99.844
4.048-4.5240.19300.131553X-RAY DIFFRACTION100
4.524-5.2190.176360.13487X-RAY DIFFRACTION99.8092
5.219-6.3820.137190.18429X-RAY DIFFRACTION99.7773
6.382-8.9820.139130.159337X-RAY DIFFRACTION98.8701
8.982-26.4460.204150.184189X-RAY DIFFRACTION93.1507

+
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://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