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- PDB-5x9j: Structure of PrhC from Penicillium brasilianum NBRC 6234 -

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Basic information

Entry
Database: PDB / ID: 5x9j
TitleStructure of PrhC from Penicillium brasilianum NBRC 6234
ComponentsPrhC
KeywordsISOMERASE / meroterpenoid / paraherquonin
Function / homologyparaherquonin biosynthetic process / : / Isomerases / isomerase activity / Isomerase prhC
Function and homology information
Biological speciesPenicillium brasilianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMori, T. / Wang, H. / Matsuda, Y. / Abe, I.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Molecular basis for the unusual ring reconstruction in fungal meroterpenoid biogenesis
Authors: Mori, T. / Iwabuchi, T. / Hoshino, S. / Wang, H. / Matsuda, Y. / Abe, I.
History
DepositionMar 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Sep 16, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 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: PrhC
B: PrhC


Theoretical massNumber of molelcules
Total (without water)42,9082
Polymers42,9082
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-15 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.064, 157.064, 49.716
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PrhC


Mass: 21454.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium brasilianum (fungus) / Gene: prhC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E1FFL1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM HEPES (pH 7.5), 1.125M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 41556 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 22.19
Reflection shellResolution: 2.09→2.22 Å / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 4.35 / Num. unique obs: 6597 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WQF

5wqf


Resolution: 2.1→46.695 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.95
RfactorNum. reflection% reflection
Rfree0.2042 2006 4.86 %
Rwork0.1853 --
obs0.1862 41315 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 0 177 2563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072434
X-RAY DIFFRACTIONf_angle_d0.8013293
X-RAY DIFFRACTIONf_dihedral_angle_d14.2481453
X-RAY DIFFRACTIONf_chiral_restr0.05361
X-RAY DIFFRACTIONf_plane_restr0.004424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.26731450.22952803X-RAY DIFFRACTION100
2.1525-2.21070.23841390.20922792X-RAY DIFFRACTION100
2.2107-2.27580.29811430.20652784X-RAY DIFFRACTION100
2.2758-2.34920.2261440.19792789X-RAY DIFFRACTION100
2.3492-2.43320.20431380.19222766X-RAY DIFFRACTION100
2.4332-2.53060.24641430.20292779X-RAY DIFFRACTION100
2.5306-2.64580.23031440.19492792X-RAY DIFFRACTION100
2.6458-2.78530.22971440.20172797X-RAY DIFFRACTION100
2.7853-2.95970.21791420.20062798X-RAY DIFFRACTION100
2.9597-3.18820.22691410.1952797X-RAY DIFFRACTION100
3.1882-3.5090.20561430.18342839X-RAY DIFFRACTION100
3.509-4.01650.1791430.1662819X-RAY DIFFRACTION100
4.0165-5.05940.16581440.15772834X-RAY DIFFRACTION100
5.0594-46.70630.18551530.18872920X-RAY DIFFRACTION100

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