[English] 日本語
Yorodumi
- PDB-6on3: A substrate bound structure of L-DOPA dioxygenase from Streptomyc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6on3
TitleA substrate bound structure of L-DOPA dioxygenase from Streptomyces sclerotialus
ComponentsL-DOPA extradiol dioxygenase
KeywordsOXIDOREDUCTASE / extradiol dioxygenase / vincinal oxygen chelate superfamily.
Function / homologyGlyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / 3,4-DIHYDROXYPHENYLALANINE / : / L-DOPA dioxygenase
Function and homology information
Biological speciesStreptomyces sclerotialus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsWang, Y. / Shin, I. / Fu, Y. / Colabroy, K. / Liu, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1808637 United States
National Science Foundation (NSF, United States)CHE-1708237 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
CitationJournal: Biochemistry / Year: 2019
Title: Crystal Structures of L-DOPA Dioxygenase fromStreptomyces sclerotialus.
Authors: Wang, Y. / Shin, I. / Fu, Y. / Colabroy, K.L. / Liu, A.
History
DepositionApr 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-DOPA extradiol dioxygenase
B: L-DOPA extradiol dioxygenase
C: L-DOPA extradiol dioxygenase
D: L-DOPA extradiol dioxygenase
E: L-DOPA extradiol dioxygenase
F: L-DOPA extradiol dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,30023
Polymers113,1716
Non-polymers2,12917
Water5,441302
1
A: L-DOPA extradiol dioxygenase
B: L-DOPA extradiol dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,71810
Polymers37,7242
Non-polymers9958
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-43 kcal/mol
Surface area12860 Å2
MethodPISA
2
C: L-DOPA extradiol dioxygenase
D: L-DOPA extradiol dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2306
Polymers37,7242
Non-polymers5064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-55 kcal/mol
Surface area13340 Å2
MethodPISA
3
E: L-DOPA extradiol dioxygenase
F: L-DOPA extradiol dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3527
Polymers37,7242
Non-polymers6285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-53 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.830, 40.720, 128.430
Angle α, β, γ (deg.)90.00, 105.11, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
L-DOPA extradiol dioxygenase


Mass: 18861.846 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sclerotialus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5H1ZR51*PLUS
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-DAH / 3,4-DIHYDROXYPHENYLALANINE / L-DOPA


Type: L-peptide linking / Mass: 197.188 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H11NO4
#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.2 M MgCl2 and 16% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 42332 / % possible obs: 94.5 % / Biso Wilson estimate: 28.47 Å2
Reflection shellResolution: 2.31→2.35 Å / Rmerge(I) obs: 0.552 / % possible all: 82

-
Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→44.01 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.294 1999 6.2 %
Rwork0.235 --
obs-32257 72.1 %
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 2.31→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7238 0 130 302 7670
LS refinement shellResolution: 2.31→2.37 Å
RfactorNum. reflection% reflection
Rfree0.4394 36 -
Rwork0.288 533 -
obs--18 %

+
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