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- PDB-6kd0: Crystal Structure of Vibralactone Cyclase -

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Basic information

Entry
Database: PDB / ID: 6kd0
TitleCrystal Structure of Vibralactone Cyclase
ComponentsVibralactone Cyclase
KeywordsHYDROLASE / Vibralactone Cyclase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesBoreostereum vibrans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZeng, Y. / Feng, K.N.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: A Hydrolase-Catalyzed Cyclization Forms the Fused Bicyclic beta-Lactone in Vibralactone.
Authors: Feng, K.N. / Yang, Y.L. / Xu, Y.X. / Zhang, Y. / Feng, T. / Huang, S.X. / Liu, J.K. / Zeng, Y.
History
DepositionJun 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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: Vibralactone Cyclase


Theoretical massNumber of molelcules
Total (without water)38,7191
Polymers38,7191
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14480 Å2
Unit cell
Length a, b, c (Å)47.324, 80.234, 59.184
Angle α, β, γ (deg.)90.00, 102.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vibralactone Cyclase


Mass: 38718.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Boreostereum vibrans (fungus) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 39851 / % possible obs: 100 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.064 / Net I/σ(I): 13.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1915 / Rpim(I) all: 0.423 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LK6

5lk6


Resolution: 1.8→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1987 2019 5.07 %
Rwork0.18 --
obs-37766 100 %
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 0 268 2996
LS refinement shellResolution: 1.8→1.84 Å
RfactorNum. reflection% reflection
Rfree0.2 --
Rwork0.17 --
obs-2504 92 %

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