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- PDB-5no5: AbyA5 Wildtype -

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Basic information

Entry
Database: PDB / ID: 5no5
TitleAbyA5 Wildtype
ComponentsAbyA5
KeywordsHYDROLASE / Deacetylase / Elimination / Spirotetronate / Acetyl Lyase
Function / homologyEsterase FrsA-like / Esterase FrsA-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / AbyA5
Function and homology information
Biological speciesVerrucosispora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsByrne, M.J. / Race, P.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/D526037/ 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
DepositionApr 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 12, 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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: AbyA5
B: AbyA5


Theoretical massNumber of molelcules
Total (without water)81,5542
Polymers81,5542
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-6 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.229, 88.360, 131.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AbyA5


Mass: 40776.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrucosispora (bacteria) / Gene: abyA5, VAB18032_16440 / Production host: Escherichia coli B (bacteria) / Variant (production host): B834 / References: UniProt: F4F7F5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Wild type AbyA5 data sets were collected from crystals formed in formed in 12.5 % w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M ...Details: Wild type AbyA5 data sets were collected from crystals formed in formed in 12.5 % w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, HCl, 0.02 M DL-serine, 0.1 M Bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 65 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97887 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 2.5→41.93 Å / Num. obs: 27564 / % possible obs: 96.6 % / Redundancy: 11.8 % / Net I/σ(I): 7.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YWF

4ywf


Resolution: 2.5→73.3 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.003 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.592 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 1356 4.9 %RANDOM
Rwork0.20812 ---
obs0.21079 26076 96.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.384 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å2-0 Å20 Å2
2--3.57 Å2-0 Å2
3----1.14 Å2
Refinement stepCycle: 1 / Resolution: 2.5→73.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5301 0 0 98 5399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195438
X-RAY DIFFRACTIONr_bond_other_d0.0020.025067
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9497445
X-RAY DIFFRACTIONr_angle_other_deg1.081311607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2245696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.42322.116241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4315780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3041560
X-RAY DIFFRACTIONr_chiral_restr0.0960.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216184
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021192
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_it0.9031.592790
X-RAY DIFFRACTIONr_mcbond_other0.9031.5892789
X-RAY DIFFRACTIONr_mcangle_it1.5022.3823484
X-RAY DIFFRACTIONr_mcangle_other1.5022.3833485
X-RAY DIFFRACTIONr_scbond_it1.2851.752648
X-RAY DIFFRACTIONr_scbond_other1.2851.752646
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1232.5613961
X-RAY DIFFRACTIONr_long_range_B_refined3.05718.7495927
X-RAY DIFFRACTIONr_long_range_B_other3.04918.7565916
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 106 -
Rwork0.248 1898 -
obs--95.66 %

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