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- PDB-7vbq: Heterodimer structure of Fe(II)/(alpha)ketoglutarate-dependent di... -

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Basic information

Entry
Database: PDB / ID: 7vbq
TitleHeterodimer structure of Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxIJ
Components
  • Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI
  • Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxJ
KeywordsOXIDOREDUCTASE / Fe(II)/(alpha)ketoglutarate-dependent dioxygenase / heterodimer
Function / homologyq2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta / : / N-OXALYLGLYCINE
Function and homology information
Biological speciesTalaromyces purpureogenus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLi, X. / Awakawa, T. / Mori, T. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Heterodimeric Non-heme Iron Enzymes in Fungal Meroterpenoid Biosynthesis.
Authors: Li, X. / Awakawa, T. / Mori, T. / Ling, M. / Hu, D. / Wu, B. / Abe, I.
History
DepositionSep 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxJ
B: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8976
Polymers67,5822
Non-polymers3154
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-57 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.933, 75.335, 133.611
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 Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxJ


Mass: 35905.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces purpureogenus (fungus) / Production host: Escherichia coli (E. coli)
#2: Protein Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI


Mass: 31676.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces purpureogenus (fungus) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl (PH 7.2), 20% (w/v) PEG 3350, 200mM Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.42 Å / Num. obs: 43789 / % possible obs: 99.2 % / Redundancy: 15.3 % / Biso Wilson estimate: 21.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.201 / Net I/σ(I): 13.1
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 1.456 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3021 / CC1/2: 0.831

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zm2

5zm2


Resolution: 1.95→46.42 Å / SU ML: 0.1801 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2137 1890 4.53 %
Rwork0.1706 39824 -
obs0.1726 41714 94.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.94 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 13 430 4775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764454
X-RAY DIFFRACTIONf_angle_d0.95526049
X-RAY DIFFRACTIONf_chiral_restr0.0567651
X-RAY DIFFRACTIONf_plane_restr0.0085798
X-RAY DIFFRACTIONf_dihedral_angle_d15.73271638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.29091320.23092678X-RAY DIFFRACTION84.13
2-2.060.27471320.19742774X-RAY DIFFRACTION87.4
2.06-2.130.26231320.1942880X-RAY DIFFRACTION89.32
2.13-2.20.25311310.18762902X-RAY DIFFRACTION90.94
2.2-2.290.20531400.17863001X-RAY DIFFRACTION93.23
2.29-2.40.24581500.17753050X-RAY DIFFRACTION94.96
2.4-2.520.25071480.17693060X-RAY DIFFRACTION95.33
2.52-2.680.22211480.17343117X-RAY DIFFRACTION96.51
2.68-2.890.21461480.17873165X-RAY DIFFRACTION97.7
2.89-3.180.18771510.183197X-RAY DIFFRACTION98.53
3.18-3.640.22041560.16243246X-RAY DIFFRACTION99.39
3.64-4.580.17271570.1373306X-RAY DIFFRACTION99.8
4.58-46.420.19671650.17013448X-RAY DIFFRACTION99.83

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