[English] 日本語
Yorodumi
- PDB-6elv: Recombinantly expressed C-terminal domain of MdPPO1 (Csole-domain) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6elv
TitleRecombinantly expressed C-terminal domain of MdPPO1 (Csole-domain)
ComponentsPolyphenol oxidase, chloroplastic
KeywordsOXIDOREDUCTASE / polyphenol oxidase / tyrosinase / C-temrinal domain / autolysis
Function / homology
Function and homology information


catechol oxidase / catechol oxidase activity / pigment biosynthetic process / chloroplast thylakoid lumen / metal ion binding
Similarity search - Function
Polyphenol oxidase / Polyphenol oxidase, C-terminal / Protein of unknown function (DUF_B2219) / Polyphenol oxidase, central domain / Polyphenol oxidase middle domain / Tyrosinase CuA-binding region signature. / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily
Similarity search - Domain/homology
Polyphenol oxidase, chloroplastic
Similarity search - Component
Biological speciesMalus domestica (apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsKampatsikas, I. / Bijelic, A. / Pretzler, M. / Rompel, A.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP25217 Austria
Austrian Science FundP29144 Austria
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: A Peptide-Induced Self-Cleavage Reaction Initiates the Activation of Tyrosinase.
Authors: Kampatsikas, I. / Bijelic, A. / Pretzler, M. / Rompel, A.
History
DepositionSep 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyphenol oxidase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8373
Polymers15,7611
Non-polymers762
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-18 kcal/mol
Surface area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.130, 50.100, 50.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Polyphenol oxidase, chloroplastic / Catechol oxidase


Mass: 15761.013 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malus domestica (apple) / Production host: Escherichia coli (E. coli) / References: UniProt: P43309*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.81 Å3/Da / Density % sol: 32.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15 mg/ml, 100 mM TRIS-HCl pH 8.25, 13 % PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.05→50.54 Å / Num. obs: 51007 / % possible obs: 94.1 % / Redundancy: 11.3 % / Rpim(I) all: 0.05785 / Rrim(I) all: 0.016 / Net I/σ(I): 20.85
Reflection shellResolution: 1.05→1.08 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3333 / Rpim(I) all: 0.5716 / Rrim(I) all: 0.248 / % possible all: 54

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: latent MdPPO1

Resolution: 1.05→35.581 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.51
RfactorNum. reflection% reflection
Rfree0.1607 2551 5 %
Rwork0.1476 --
obs0.1482 51002 94.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.05→35.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 2 233 1265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071066
X-RAY DIFFRACTIONf_angle_d0.9871445
X-RAY DIFFRACTIONf_dihedral_angle_d14.3410
X-RAY DIFFRACTIONf_chiral_restr0.097172
X-RAY DIFFRACTIONf_plane_restr0.005185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.07020.2371860.20881624X-RAY DIFFRACTION58
1.0702-1.0920.21051030.17941956X-RAY DIFFRACTION69
1.092-1.11580.19041180.14922252X-RAY DIFFRACTION80
1.1158-1.14170.13361340.12832539X-RAY DIFFRACTION90
1.1417-1.17030.14881450.12032748X-RAY DIFFRACTION97
1.1703-1.20190.14411490.11232839X-RAY DIFFRACTION100
1.2019-1.23730.13941480.11422807X-RAY DIFFRACTION100
1.2373-1.27730.14051500.11382862X-RAY DIFFRACTION100
1.2773-1.32290.1461490.11172818X-RAY DIFFRACTION100
1.3229-1.37590.14971490.11712844X-RAY DIFFRACTION100
1.3759-1.43850.15061500.11852839X-RAY DIFFRACTION100
1.4385-1.51430.14861490.12082839X-RAY DIFFRACTION100
1.5143-1.60920.13271510.12482869X-RAY DIFFRACTION100
1.6092-1.73350.15241510.1352868X-RAY DIFFRACTION100
1.7335-1.90790.16361510.14392855X-RAY DIFFRACTION100
1.9079-2.18390.14511520.14612906X-RAY DIFFRACTION100
2.1839-2.75140.2111540.17462921X-RAY DIFFRACTION100
2.7514-35.6010.15661620.16753065X-RAY DIFFRACTION100

+
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