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- PDB-9ig4: Crystal structure of Fe/alphaKG-Dependent Decarboxylase TraH in c... -

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Basic information

Entry
Database: PDB / ID: 9ig4
TitleCrystal structure of Fe/alphaKG-Dependent Decarboxylase TraH in complexes with Mn2+
Components2-oxoglutarate-dependent dioxygenase traH
KeywordsOXIDOREDUCTASE / Fe/alphaKG-Dependent Decarboxylase / Metal Binding / Complex
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
: / 2-oxoglutarate-dependent dioxygenase traH
Similarity search - Component
Biological speciesPenicillium crustosum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,2024
Polymers75,0932
Non-polymers1102
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-6 kcal/mol
Surface area24790 Å2
Unit cell
Length a, b, c (Å)77.210, 77.210, 223.550
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

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Components

#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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1M Sodium cacodylate pH 6.5, 5%(w/v) PEG 8000, 40%(v/v) MPD

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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: 2.1→49.06 Å / Num. obs: 75250 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 38.59 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.58
Reflection shellResolution: 2.1→2.23 Å / Num. unique obs: 12176 / CC1/2: 0.841

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Processing

Software
NameVersionClassification
PHENIXdev.3206refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.06 Å / SU ML: 0.239 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.92
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2364 2022 5 %
Rwork0.1985 38419 -
obs0.2004 40441 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.84 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4486 0 2 205 4693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714617
X-RAY DIFFRACTIONf_angle_d0.87856250
X-RAY DIFFRACTIONf_chiral_restr0.0524655
X-RAY DIFFRACTIONf_plane_restr0.0088807
X-RAY DIFFRACTIONf_dihedral_angle_d14.79841682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.26721420.22812689X-RAY DIFFRACTION99.82
2.15-2.210.29391420.23162693X-RAY DIFFRACTION100
2.21-2.280.28431410.23162689X-RAY DIFFRACTION100
2.28-2.350.25741420.21892690X-RAY DIFFRACTION100
2.35-2.430.25951420.22452697X-RAY DIFFRACTION100
2.43-2.530.30011410.21512693X-RAY DIFFRACTION100
2.53-2.650.27031440.21992721X-RAY DIFFRACTION99.97
2.65-2.790.26111430.20632721X-RAY DIFFRACTION100
2.79-2.960.2521440.21622735X-RAY DIFFRACTION100
2.96-3.190.26711440.21842735X-RAY DIFFRACTION99.93
3.19-3.510.24451450.20552763X-RAY DIFFRACTION99.9
3.51-4.020.22231460.17582777X-RAY DIFFRACTION99.97
4.02-5.060.19121480.16262815X-RAY DIFFRACTION99.97
5.06-49.060.2221580.20263001X-RAY DIFFRACTION99.75

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