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

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Basic information

Entry
Database: PDB / ID: 5ybn
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA in complex with (alpha)ketoglutarate
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
2-OXOGLUTARIC ACID / : / Multifunctional dioxygenase prhA
Similarity search - Component
Biological speciesPenicillium brasilianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.104 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)70,7376
Polymers70,3342
Non-polymers4044
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-46 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.350, 172.350, 45.291
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.95 Å3/Da / Density % sol: 58.33 %
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 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→43.1 Å / Num. obs: 44951 / % possible obs: 99.6 % / Redundancy: 3.5 % / Net I/σ(I): 17.1
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: 5YBM

5ybm


Resolution: 2.104→43.087 Å / Cross valid method: FREE R-VALUE / Phase error: 24.52
RfactorNum. reflection% reflection
Rfree0.225 1996 4.44 %
Rwork0.1862 --
obs0.1881 44951 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.104→43.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4457 0 22 327 4806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064620
X-RAY DIFFRACTIONf_angle_d0.816276
X-RAY DIFFRACTIONf_dihedral_angle_d19.9412772
X-RAY DIFFRACTIONf_chiral_restr0.052668
X-RAY DIFFRACTIONf_plane_restr0.007848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1056-2.15830.31811430.27483066X-RAY DIFFRACTION95
2.1583-2.21660.32481400.26443004X-RAY DIFFRACTION95
2.2166-2.28190.30881420.25493051X-RAY DIFFRACTION95
2.2819-2.35550.30861400.25083023X-RAY DIFFRACTION95
2.3555-2.43970.28631460.22923043X-RAY DIFFRACTION95
2.4397-2.53740.28631410.22773057X-RAY DIFFRACTION95
2.5374-2.65280.271420.22163054X-RAY DIFFRACTION95
2.6528-2.79270.24351420.21653044X-RAY DIFFRACTION95
2.7927-2.96760.2151410.20833060X-RAY DIFFRACTION95
2.9676-3.19660.2361380.18553077X-RAY DIFFRACTION96
3.1966-3.51820.21241430.17093068X-RAY DIFFRACTION95
3.5182-4.02690.17411430.14813082X-RAY DIFFRACTION95
4.0269-5.0720.15491450.13513109X-RAY DIFFRACTION95
5.072-41.40510.24811470.18193183X-RAY DIFFRACTION95

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