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- PDB-7vbr: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI -

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Basic information

Entry
Database: PDB / ID: 7vbr
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI
ComponentsFe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI
KeywordsOXIDOREDUCTASE / Fe(II)/(alpha)ketoglutarate-dependent dioxygenase
Function / homologyq2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesTalaromyces purpureogenus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 TlxI
B: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI
D: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI
C: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI


Theoretical massNumber of molelcules
Total (without water)126,7074
Polymers126,7074
Non-polymers00
Water6,774376
1
A: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI


Theoretical massNumber of molelcules
Total (without water)31,6771
Polymers31,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI


Theoretical massNumber of molelcules
Total (without water)31,6771
Polymers31,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI


Theoretical massNumber of molelcules
Total (without water)31,6771
Polymers31,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI


Theoretical massNumber of molelcules
Total (without water)31,6771
Polymers31,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.403, 64.450, 76.988
Angle α, β, γ (deg.)81.750, 73.705, 74.825
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI


Mass: 31676.865 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces purpureogenus (fungus) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-Tris (PH 6.5), 2% (v/v) Tacsimate (PH 6.0), 20% (w/v) PEG 3350

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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: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.32 Å / Num. obs: 65297 / % possible obs: 97.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.1
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4485 / CC1/2: 0.601

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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: 2.1→49.32 Å / SU ML: 0.2964 / Cross valid method: FREE R-VALUE / σ(F): 1.76 / Phase error: 28.3009
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.254 1999 3.06 %
Rwork0.2087 63285 -
obs0.2101 65284 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7383 0 0 376 7759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817574
X-RAY DIFFRACTIONf_angle_d0.910610288
X-RAY DIFFRACTIONf_chiral_restr0.05331139
X-RAY DIFFRACTIONf_plane_restr0.00671348
X-RAY DIFFRACTIONf_dihedral_angle_d16.60762733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.32511390.274401X-RAY DIFFRACTION94.7
2.15-2.210.30431410.25814462X-RAY DIFFRACTION96.72
2.21-2.270.28841420.24994492X-RAY DIFFRACTION96.88
2.27-2.350.29961410.24154456X-RAY DIFFRACTION97.04
2.35-2.430.35521430.24434533X-RAY DIFFRACTION97.27
2.43-2.530.33841430.24384515X-RAY DIFFRACTION97.51
2.53-2.640.28531430.23284539X-RAY DIFFRACTION97.64
2.64-2.780.31591430.23174539X-RAY DIFFRACTION97.83
2.78-2.960.3011430.2364533X-RAY DIFFRACTION98.01
2.96-3.190.28741440.22234548X-RAY DIFFRACTION98.14
3.19-3.510.26321420.20924500X-RAY DIFFRACTION97.73
3.51-4.010.22231440.18414577X-RAY DIFFRACTION98.48
4.01-5.060.18541450.16154572X-RAY DIFFRACTION99.06
5.06-49.320.2041460.19244618X-RAY DIFFRACTION99.29

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