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- PDB-4ywf: AbyA5 -

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Basic information

Entry
Database: PDB / ID: 4ywf
TitleAbyA5
ComponentsAbyA5
KeywordsHYDROLASE / Deacetylase / Elimination / Spirotetronate
Function / homologyEsterase FrsA-like / Esterase FrsA-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / AbyA5
Function and homology information
Biological speciesVerrucosispora maris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsByrne, M.J. / Race, P.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: An Esterase-like Lyase Catalyzes Acetate Elimination in Spirotetronate/Spirotetramate Biosynthesis.
Authors: Lees, N.R. / Han, L.C. / Byrne, M.J. / Davies, J.A. / Parnell, A.E. / Moreland, P.E.J. / Stach, J.E.M. / van der Kamp, M.W. / Willis, C.L. / Race, P.R.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AbyA5


Theoretical massNumber of molelcules
Total (without water)41,2241
Polymers41,2241
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.080, 87.180, 47.910
Angle α, β, γ (deg.)90.00, 101.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AbyA5


Mass: 41224.289 Da / Num. of mol.: 1 / Mutation: L66M, L158M, L195M, L295M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrucosispora maris (bacteria) / Gene: abyA5, VAB18032_16440 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4F7F5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02M magnesium chloride, 0.1M HEPES, 22% w/v polyacrylic acid 5100 sodium salt, pH 7.5
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97957 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2→36.39 Å / Num. obs: 25075 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 3.4
Reflection shellRmerge(I) obs: 0.29

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Aimlessdata scaling
PHENIXphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2→36.39 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.395 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23643 1275 5.1 %RANDOM
Rwork0.21789 ---
obs0.21883 23787 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.237 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å20.76 Å2
2--1.08 Å20 Å2
3----3.54 Å2
Refinement stepCycle: 1 / Resolution: 2→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 0 50 2543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192556
X-RAY DIFFRACTIONr_bond_other_d0.0010.022381
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.9583501
X-RAY DIFFRACTIONr_angle_other_deg2.06235433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26622.075106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64815333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4721525
X-RAY DIFFRACTIONr_chiral_restr0.0990.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212933
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02592
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4193.0441330
X-RAY DIFFRACTIONr_mcbond_other2.4123.0431329
X-RAY DIFFRACTIONr_mcangle_it3.2534.5551659
X-RAY DIFFRACTIONr_mcangle_other3.2554.5561660
X-RAY DIFFRACTIONr_scbond_it3.0863.3121226
X-RAY DIFFRACTIONr_scbond_other3.0843.3121227
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2674.8631843
X-RAY DIFFRACTIONr_long_range_B_refined5.91325.4272880
X-RAY DIFFRACTIONr_long_range_B_other5.91225.3612867
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 102 -
Rwork0.278 1758 -
obs--99.95 %

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