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- PDB-7eeh: Selenomethionine labeled Fe(II)/(alpha)ketoglutarate-dependent di... -

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Basic information

Entry
Database: PDB / ID: 7eeh
TitleSelenomethionine labeled Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TqaL
ComponentsTqaL
KeywordsOXIDOREDUCTASE / alpha-ketoglutarate dependent dioxygenase / aziridine / biosynthesis
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
2OG-Fe dioxygenase / 2OG-Fe dioxygenase / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Uncharacterized protein B14A6.180
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBunno, R. / Mori, T. / Awakawa, T. / Abe, I.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Aziridine Formation by a Fe II / alpha-Ketoglutarate Dependent Oxygenase and 2-Aminoisobutyrate Biosynthesis in Fungi.
Authors: Bunno, R. / Awakawa, T. / Mori, T. / Abe, I.
History
DepositionMar 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: 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.name
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TqaL
B: TqaL
C: TqaL
D: TqaL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,64512
Polymers143,9334
Non-polymers7128
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-73 kcal/mol
Surface area47170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.746, 99.488, 193.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
TqaL


Mass: 35983.191 Da / Num. of mol.: 4 / Mutation: K82M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: B14A6.180 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8X0D9
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 100 mM Tris-HCl (pH 7.75), 0.2 M MgCl2, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.07 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2→48.48 Å / Num. obs: 104375 / % possible obs: 99.7 % / Redundancy: 15.2 % / Biso Wilson estimate: 27.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 1.527 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4910 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→48.48 Å / SU ML: 0.2445 / Cross valid method: FREE R-VALUE / σ(F): 1.78 / Phase error: 32.1502
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2609 1989 1.92 %
Rwork0.2322 101655 -
obs0.2328 103644 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.58 Å2
Refinement stepCycle: LAST / Resolution: 2→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8750 0 36 455 9241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00838967
X-RAY DIFFRACTIONf_angle_d0.973112130
X-RAY DIFFRACTIONf_chiral_restr0.05361371
X-RAY DIFFRACTIONf_plane_restr0.00561567
X-RAY DIFFRACTIONf_dihedral_angle_d14.58333367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.36541360.3226998X-RAY DIFFRACTION96.9
2.05-2.110.3381420.28997184X-RAY DIFFRACTION99.35
2.11-2.170.27021410.27527203X-RAY DIFFRACTION99.46
2.17-2.240.29421420.25517238X-RAY DIFFRACTION99.64
2.24-2.320.27021410.24617252X-RAY DIFFRACTION99.72
2.32-2.410.2881430.24667236X-RAY DIFFRACTION99.43
2.41-2.520.29711410.25437205X-RAY DIFFRACTION99.5
2.52-2.650.27821440.24377273X-RAY DIFFRACTION99.53
2.65-2.820.24831410.23647265X-RAY DIFFRACTION99.69
2.82-3.040.3071420.24867286X-RAY DIFFRACTION99.37
3.04-3.340.23051440.24217255X-RAY DIFFRACTION98.76
3.34-3.830.22431430.22747313X-RAY DIFFRACTION99.04
3.83-4.820.22111450.187412X-RAY DIFFRACTION99.62
4.82-48.480.26551440.21167535X-RAY DIFFRACTION97.5

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