[English] 日本語
Yorodumi
- PDB-9ig5: Fe/alpha-KG-Dependent Decarboxylase TraH in complexes with Mn2+, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ig5
TitleFe/alpha-KG-Dependent Decarboxylase TraH in complexes with Mn2+, alpha-KG, and Substrate
Components2-oxoglutarate-dependent dioxygenase traH
KeywordsOXIDOREDUCTASE / Fe/alpha-KG-Dependent Decarboxylase / Complex / Alpha-Ketoglutarate / Substrate / Metal Binding
Function / homology
Function and homology information


small molecule biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / dioxygenase activity / metal ion binding
Similarity search - Function
: / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
Chem-1PG / : / 2-OXOGLUTARIC ACID / : / TRIETHYLENE GLYCOL / 2-oxoglutarate-dependent dioxygenase traH
Similarity search - Component
Biological speciesPenicillium crustosum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZheng, X. / Zheng, L. / Bange, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: A Novel Catalytic Mechanism of Lid Loop-Mediated Proton Transfer Revealed in the Fe/alpha-KG-Dependent Decarboxylase TraH
Authors: Zheng, X. / Zheng, L. / Bange, G.
History
DepositionFeb 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-oxoglutarate-dependent dioxygenase traH
B: 2-oxoglutarate-dependent dioxygenase traH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,42610
Polymers75,0932
Non-polymers1,3338
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint8 kcal/mol
Surface area25160 Å2
Unit cell
Length a, b, c (Å)77.210, 77.210, 225.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein 2-oxoglutarate-dependent dioxygenase traH / Terrestric acid biosynthesis cluster protein H


Mass: 37546.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium crustosum (fungus) / Gene: traH / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A481WQ18, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

-
Non-polymers , 6 types, 145 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1I31 / 2-[(2~{S})-3-oxidanyl-4-[(4~{S})-4-oxidanylhexanoyl]-5-oxidanylidene-2~{H}-furan-2-yl]ethanoic acid


Mass: 272.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.1M CHES pH 9.5, 30%(w/v) PEG 3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.4→49.15 Å / Num. obs: 50560 / % possible obs: 99.2 % / Redundancy: 13.4 % / Biso Wilson estimate: 37.75 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.45
Reflection shellResolution: 2.4→2.55 Å / Num. unique obs: 8201 / CC1/2: 0.774

-
Processing

Software
NameVersionClassification
PHENIXdev.5306refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→49.15 Å / SU ML: 0.2894 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9589
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2545 1367 5 %
Rwork0.1958 25969 -
obs0.1987 27336 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.81 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 0 85 137 5002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794993
X-RAY DIFFRACTIONf_angle_d0.94236751
X-RAY DIFFRACTIONf_chiral_restr0.0519699
X-RAY DIFFRACTIONf_plane_restr0.01878
X-RAY DIFFRACTIONf_dihedral_angle_d16.02031822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.31281330.27542542X-RAY DIFFRACTION98.31
2.49-2.590.31021350.22732550X-RAY DIFFRACTION99.67
2.59-2.70.27291340.22832549X-RAY DIFFRACTION99.67
2.7-2.850.32161360.2242591X-RAY DIFFRACTION99.82
2.85-3.020.25621360.21632583X-RAY DIFFRACTION99.96
3.03-3.260.26191360.21362586X-RAY DIFFRACTION99.49
3.26-3.590.27221360.20132579X-RAY DIFFRACTION98.69
3.59-4.10.24011350.17862561X-RAY DIFFRACTION96.77
4.11-5.170.23461360.16452577X-RAY DIFFRACTION96
5.17-49.150.22241500.17732851X-RAY DIFFRACTION99.93

+
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