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- PDB-8gr5: Cop4 from Antrodia cinnamomea in apo form -

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Basic information

Entry
Database: PDB / ID: 8gr5
TitleCop4 from Antrodia cinnamomea in apo form
ComponentsAcCop4
KeywordsLYASE / Terpenoid / cubebol
Function / homology1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
Function and homology information
Biological speciesAntrodia cinnamomea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, S.C. / Hsu, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2628-B-002-049 Taiwan
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Characterization and Crystal Structures of a Cubebol-Producing Sesquiterpene Synthase from Antrodia cinnamomea .
Authors: Chen, S.C. / Jiang, B.C. / Lu, Y.J. / Chang, C.H. / Wu, T.H. / Lin, S.W. / Yin, H.W. / Lee, T.H. / Hsu, C.H.
History
DepositionSep 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AcCop4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9857
Polymers39,3621
Non-polymers6236
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint4 kcal/mol
Surface area13900 Å2
Unit cell
Length a, b, c (Å)68.239, 59.768, 85.221
Angle α, β, γ (deg.)90.000, 110.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AcCop4


Mass: 39362.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Antrodia cinnamomea (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: HEPES pH 7.5, 10% 2-Propanol, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.03
ReflectionResolution: 2.1→30 Å / Num. obs: 18357 / % possible obs: 99 % / Redundancy: 6.6 % / Rrim(I) all: 0.133 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 1827 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OFL

7ofl


Resolution: 2.1→27.98 Å / Cross valid method: THROUGHOUT / σ(F): 33.95 / Phase error: 23.91 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2239 1868 10.56 %
Rwork0.1888 15882 -
obs0.1947 17695 93.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.75 Å2 / Biso mean: 26.4348 Å2 / Biso min: 12.96 Å2
Refinement stepCycle: final / Resolution: 2.1→27.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 41 166 2770
Biso mean--40.86 37.36 -
Num. residues----319
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.314 103 -
Rwork0.252 897 -
all-1000 -
obs--62 %

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