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- PDB-5ybm: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA -

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Basic information

Entry
Database: PDB / ID: 5ybm
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA
ComponentsPrhA
KeywordsOXIDOREDUCTASE / dioxygenase / apo
Function / homology
Function and homology information


paraherquonin biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / dioxygenase activity / metal ion binding
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Multifunctional dioxygenase prhA
Similarity search - Component
Biological speciesPenicillium brasilianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.115 Å
AuthorsNakashima, Y. / Senda, M.
CitationJournal: Nat Commun / Year: 2018
Title: Structure function and engineering of multifunctional non-heme iron dependent oxygenases in fungal meroterpenoid biosynthesis.
Authors: Nakashima, Y. / Mori, T. / Nakamura, H. / Awakawa, T. / Hoshino, S. / Senda, M. / Senda, T. / Abe, I.
History
DepositionSep 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PrhA
B: PrhA


Theoretical massNumber of molelcules
Total (without water)70,3342
Polymers70,3342
Non-polymers00
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-21 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.834, 172.834, 44.705
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein PrhA


Mass: 35166.781 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 6-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium brasilianum (fungus) / Gene: prhA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E1FFL0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, lithium citrate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→45 Å / Num. obs: 44042 / % possible obs: 99.8 % / Redundancy: 5.7 % / Net I/σ(I): 9.1
Reflection shellResolution: 2.1→2.2 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata processing
Aimlessdata scaling
PHENIX(1.10.1_2155)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YBL

5ybl


Resolution: 2.115→43.208 Å / Cross valid method: FREE R-VALUE / Phase error: 25.03
RfactorNum. reflection% reflection
Rfree0.2291 2015 4.58 %
Rwork0.1876 --
obs0.1894 44042 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.115→43.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4438 0 0 328 4766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074564
X-RAY DIFFRACTIONf_angle_d0.8286206
X-RAY DIFFRACTIONf_dihedral_angle_d17.952728
X-RAY DIFFRACTIONf_chiral_restr0.054666
X-RAY DIFFRACTIONf_plane_restr0.006836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1163-2.16920.30321380.29782927X-RAY DIFFRACTION95
2.1692-2.22780.29021430.28782989X-RAY DIFFRACTION95
2.2278-2.29340.30981420.27362971X-RAY DIFFRACTION95
2.2934-2.36740.23711420.25962997X-RAY DIFFRACTION95
2.3674-2.45190.28261400.24552955X-RAY DIFFRACTION95
2.4519-2.550.27121460.24532987X-RAY DIFFRACTION95
2.55-2.6660.29021460.22753009X-RAY DIFFRACTION95
2.666-2.80650.27651430.22352982X-RAY DIFFRACTION95
2.8065-2.98210.2361460.20833008X-RAY DIFFRACTION95
2.9821-3.21210.24411450.1792988X-RAY DIFFRACTION95
3.2121-3.53480.19431410.16652980X-RAY DIFFRACTION95
3.5348-4.04510.19761420.14133032X-RAY DIFFRACTION95
4.0451-5.09180.1831420.12583036X-RAY DIFFRACTION95
5.0918-28.80830.20251510.17123130X-RAY DIFFRACTION95

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