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- PDB-5ybq: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA-V150L/A232... -

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Basic information

Entry
Database: PDB / ID: 5ybq
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA-V150L/A232S in complex with preaustinoid A2
ComponentsPrhA
KeywordsOXIDOREDUCTASE / alpha-kegoglutarate-dependent dioxygenase
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)
Similarity search - Domain/homology
preaustinoid A2 / 2-OXOGLUTARIC ACID / : / Multifunctional dioxygenase prhA
Similarity search - Component
Biological speciesPenicillium brasilianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PrhA
B: PrhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7158
Polymers70,3942
Non-polymers1,3216
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-50 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.361, 171.361, 45.559
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: 35196.809 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 6-294 / Mutation: V150L, A232S
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: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-8T0 / preaustinoid A2


Mass: 458.544 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H34O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
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: NSRRC / Beamline: BL17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→49 Å / Num. obs: 36757 / % possible obs: 99.8 % / Redundancy: 5 % / Net I/σ(I): 14.3
Reflection shellResolution: 2.25→2.32 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: 5YBM

5ybm


Resolution: 2.25→43.553 Å / Cross valid method: FREE R-VALUE / Phase error: 29.65
RfactorNum. reflection% reflection
Rfree0.255 2009 5.47 %
Rwork0.2071 --
obs0.2098 36757 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→43.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4330 0 88 191 4609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084551
X-RAY DIFFRACTIONf_angle_d0.9426216
X-RAY DIFFRACTIONf_dihedral_angle_d19.4292666
X-RAY DIFFRACTIONf_chiral_restr0.053663
X-RAY DIFFRACTIONf_plane_restr0.007833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2507-2.3070.40651420.32452457X-RAY DIFFRACTION94
2.307-2.36940.33541420.29722455X-RAY DIFFRACTION94
2.3694-2.43910.33761410.27332445X-RAY DIFFRACTION94
2.4391-2.51780.29361460.27412467X-RAY DIFFRACTION94
2.5178-2.60770.27741410.27092430X-RAY DIFFRACTION94
2.6077-2.71210.30091380.26782461X-RAY DIFFRACTION95
2.7121-2.83550.34311460.25642477X-RAY DIFFRACTION94
2.8355-2.98490.30911430.2362458X-RAY DIFFRACTION94
2.9849-3.17180.2711470.21782486X-RAY DIFFRACTION94
3.1718-3.41650.2551430.20732466X-RAY DIFFRACTION94
3.4165-3.75990.22831440.18532493X-RAY DIFFRACTION95
3.7599-4.3030.20851430.16062503X-RAY DIFFRACTION95
4.303-5.41780.1831410.16072507X-RAY DIFFRACTION95
5.4178-34.04990.25831500.18752607X-RAY DIFFRACTION94

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