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- PDB-5x9k: Structure of AusH from Aspergillus nidulans -

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Basic information

Entry
Database: PDB / ID: 5x9k
TitleStructure of AusH from Aspergillus nidulans
ComponentsAustinol synthesis protein H
KeywordsISOMERASE / meroterpenoid / Austinol
Function / homologyaustinol biosynthetic process / dehydroaustinol biosynthetic process / : / terpenoid biosynthetic process / Austinoid biosynthesis clusters protein H
Function and homology information
Biological speciesEmericella nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsIwabuchi, T. / 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: Austinol synthesis protein H
B: Austinol synthesis protein H


Theoretical massNumber of molelcules
Total (without water)37,8032
Polymers37,8032
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-13 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.589, 37.423, 74.777
Angle α, β, γ (deg.)90.00, 107.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Austinol synthesis protein H


Mass: 18901.297 Da / Num. of mol.: 2 / Fragment: UNP residues 46-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans FGSC A4 (mold) / Strain: FGSC A4 / Gene: ausH, AN9249 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5AR31
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 1.79 Å3/Da / Density % sol: 31.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Imidazole (pH 8.0), 10% PEG8000, 100 mM Ca(OAc)2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.798→50 Å / Num. obs: 25080 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.19
Reflection shellResolution: 1.798→1.91 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 3956 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WQF

5wqf


Resolution: 1.798→47.055 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.61
RfactorNum. reflection% reflection
Rfree0.2503 1992 7.94 %
Rwork0.1961 --
obs0.2004 25077 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.798→47.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 0 219 2547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072380
X-RAY DIFFRACTIONf_angle_d0.8823209
X-RAY DIFFRACTIONf_dihedral_angle_d13.0291432
X-RAY DIFFRACTIONf_chiral_restr0.053345
X-RAY DIFFRACTIONf_plane_restr0.005422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.84290.32731380.29551554X-RAY DIFFRACTION97
1.8429-1.89270.32221470.27341644X-RAY DIFFRACTION100
1.8927-1.94840.30961370.25331656X-RAY DIFFRACTION100
1.9484-2.01130.30561420.22641623X-RAY DIFFRACTION100
2.0113-2.08320.29071430.22791659X-RAY DIFFRACTION100
2.0832-2.16660.30091290.21751639X-RAY DIFFRACTION100
2.1666-2.26520.26261500.20191638X-RAY DIFFRACTION100
2.2652-2.38470.28181420.2061635X-RAY DIFFRACTION100
2.3847-2.53410.2961460.21851658X-RAY DIFFRACTION100
2.5341-2.72970.30541390.21251648X-RAY DIFFRACTION100
2.7297-3.00440.26551430.20221666X-RAY DIFFRACTION100
3.0044-3.4390.22031420.19541667X-RAY DIFFRACTION100
3.439-4.33230.2061460.15581665X-RAY DIFFRACTION99
4.3323-47.07120.19671480.16411733X-RAY DIFFRACTION99

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