[English] 日本語
Yorodumi
- PDB-5ybl: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AusE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ybl
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase AusE
ComponentsMultifunctional dioxygenase ausE
KeywordsOXIDOREDUCTASE / alpha-kegoglutarate-dependent dioxygenase
Function / homology
Function and homology information


austinol biosynthetic process / dehydroaustinol biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / terpenoid biosynthetic process / dioxygenase activity / metal ion binding
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Multifunctional dioxygenase ausE
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.108 Å
AuthorsNakashima, Y. / Senda, M.
CitationJournal: Nat Commun / Year: 2018
Title: Structure function and engineering of multifunctional non-heme iron dependent oxygenases in fungal meroterpenoid biosynthesis.
Authors: Nakashima, Y. / Mori, T. / Nakamura, H. / Awakawa, T. / Hoshino, S. / Senda, M. / Senda, T. / Abe, I.
History
DepositionSep 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multifunctional dioxygenase ausE
B: Multifunctional dioxygenase ausE
C: Multifunctional dioxygenase ausE
D: Multifunctional dioxygenase ausE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,08710
Polymers140,5754
Non-polymers5126
Water4,756264
1
A: Multifunctional dioxygenase ausE
D: Multifunctional dioxygenase ausE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5435
Polymers70,2872
Non-polymers2563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-24 kcal/mol
Surface area20060 Å2
MethodPISA
2
B: Multifunctional dioxygenase ausE
C: Multifunctional dioxygenase ausE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5435
Polymers70,2872
Non-polymers2563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-26 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.342, 223.923, 53.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

-
Components

#1: Protein
Multifunctional dioxygenase ausE / Austinol synthesis protein E


Mass: 35143.730 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 6-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ausE, AN9246 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5AR34, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, sodium citrate

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.414 Å / Num. obs: 75992 / % possible obs: 98.6 % / Redundancy: 6.8 % / Net I/σ(I): 7.4
Reflection shellResolution: 2.1→2.14 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata processing
Aimlessdata scaling
PHENIX(1.10.1_2155)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.108→48.414 Å / Cross valid method: FREE R-VALUE / Phase error: 32.02
RfactorNum. reflection% reflection
Rfree0.2657 3888 5.12 %
Rwork0.2139 --
obs0.2166 75882 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.108→48.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7863 0 24 264 8151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088079
X-RAY DIFFRACTIONf_angle_d0.97710985
X-RAY DIFFRACTIONf_dihedral_angle_d14.0964780
X-RAY DIFFRACTIONf_chiral_restr0.0551197
X-RAY DIFFRACTIONf_plane_restr0.0081459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1086-2.1450.30621550.29863341X-RAY DIFFRACTION86
2.145-2.1840.34741860.2983590X-RAY DIFFRACTION95
2.184-2.2260.31321740.28143508X-RAY DIFFRACTION92
2.226-2.27140.31971730.27913580X-RAY DIFFRACTION94
2.2714-2.32080.31391970.2753558X-RAY DIFFRACTION93
2.3208-2.37480.33112220.27443528X-RAY DIFFRACTION93
2.3748-2.43420.31341940.26733562X-RAY DIFFRACTION93
2.4342-2.50.34041610.26183616X-RAY DIFFRACTION95
2.5-2.57350.30511920.26313553X-RAY DIFFRACTION93
2.5735-2.65660.28571980.25443610X-RAY DIFFRACTION94
2.6566-2.75160.32392160.24383554X-RAY DIFFRACTION93
2.7516-2.86170.2781860.23873605X-RAY DIFFRACTION94
2.8617-2.99190.32182150.22433605X-RAY DIFFRACTION93
2.9919-3.14960.25862080.2193591X-RAY DIFFRACTION93
3.1496-3.34690.25171700.20433668X-RAY DIFFRACTION95
3.3469-3.60530.25032080.19253606X-RAY DIFFRACTION93
3.6053-3.96790.23282130.17843607X-RAY DIFFRACTION93
3.9679-4.54170.21731800.15693708X-RAY DIFFRACTION95
4.5417-5.72070.19761940.17353742X-RAY DIFFRACTION95
5.7207-48.42710.26512030.20653893X-RAY DIFFRACTION94

+
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