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- PDB-5ybo: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA in complex... -

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Basic information

Entry
Database: PDB / ID: 5ybo
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA in complex with preaustinoid A1
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) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
preaustinoid A1 / 2-OXOGLUTARIC ACID / : / Multifunctional dioxygenase prhA
Similarity search - Component
Biological speciesPenicillium brasilianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 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)71,1987
Polymers70,3342
Non-polymers8645
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-50 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.816, 171.816, 45.665
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: 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-8SX / preaustinoid A1


Mass: 460.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.96 Å3/Da / Density % sol: 58.47 %
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: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→44 Å / Num. obs: 39248 / % possible obs: 99.6 % / Redundancy: 3.5 % / Net I/σ(I): 17.5
Reflection shellResolution: 2.2→2.3 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: 2.204→43.655 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.82 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2622 2018 5.14 %
Rwork0.2126 --
obs0.2152 39248 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.204→43.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 55 183 4501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084441
X-RAY DIFFRACTIONf_angle_d0.9386054
X-RAY DIFFRACTIONf_dihedral_angle_d18.2742626
X-RAY DIFFRACTIONf_chiral_restr0.054652
X-RAY DIFFRACTIONf_plane_restr0.008814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2048-2.25990.36391440.32492636X-RAY DIFFRACTION94
2.2599-2.3210.37451370.32082618X-RAY DIFFRACTION95
2.321-2.38930.30491410.29712661X-RAY DIFFRACTION95
2.3893-2.46640.34641410.26992610X-RAY DIFFRACTION95
2.4664-2.55460.37561440.2722653X-RAY DIFFRACTION95
2.5546-2.65680.29691420.26312629X-RAY DIFFRACTION95
2.6568-2.77770.28331440.26172663X-RAY DIFFRACTION95
2.7777-2.92410.29631410.24222624X-RAY DIFFRACTION94
2.9241-3.10730.26211450.2232656X-RAY DIFFRACTION94
3.1073-3.34710.21951460.21262666X-RAY DIFFRACTION95
3.3471-3.68370.25771430.18832664X-RAY DIFFRACTION94
3.6837-4.21630.22961440.17012670X-RAY DIFFRACTION94
4.2163-5.31010.23011470.16522681X-RAY DIFFRACTION94
5.3101-40.32910.25021490.20562779X-RAY DIFFRACTION94

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