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- PDB-8zac: Crystal structure of BcABA3 from Botrytis cinerea -

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Basic information

Entry
Database: PDB / ID: 8zac
TitleCrystal structure of BcABA3 from Botrytis cinerea
ComponentsAlpha-ionylideneethane synthase aba3
KeywordsLYASE / BcABA3 / Sesquiterpene synthases / apo-form
Function / homologyabscisic acid biosynthetic process / Lyases; Carbon-oxygen lyases; Acting on phosphates / lyase activity / Alpha-ionylideneethane synthase aba3
Function and homology information
Biological speciesBotrytis cinerea B05.10 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLi, S.Y. / Li, H. / Yang, Y. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Molecular insights into a distinct class of terpenoid cyclases.
Authors: Li, S. / Huang, J.W. / Min, J. / Li, H. / Ning, M. / Zhou, S. / Yang, Y. / Chen, C.C. / Guo, R.T.
History
DepositionApr 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_initial_refinement_model / refine
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type / _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-ionylideneethane synthase aba3
B: Alpha-ionylideneethane synthase aba3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4554
Polymers106,3242
Non-polymers1312
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-30 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.203, 166.890, 57.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alpha-ionylideneethane synthase aba3 / Abscisic acid biosynthesis cluster protein 3 / Sesquiterpene synthase aba3


Mass: 53162.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Botrytis cinerea B05.10 (fungus) / Gene: aba3, BCIN_08g03880 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A384JQC9, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2% Tacsimate pH 7.0, 0.1 M HEPES pH 7.5, 25% PEG 3350

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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 MX300-HS / Detector: CCD / Date: Feb 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.45→25 Å / Num. obs: 29294 / % possible obs: 99.1 % / Redundancy: 8.5 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.018 / Rrim(I) all: 0.053 / Χ2: 1.104 / Net I/σ(I): 12.3 / Num. measured all: 250026
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.45-2.546.30.21726820.9810.9950.0890.2360.54491.9
2.54-2.648.20.19228970.9910.9980.0690.2040.55399.8
2.64-2.768.50.14929090.9920.9980.0520.1580.631100
2.76-2.98.70.11629030.9950.9990.0410.1230.70599.9
2.9-3.099.20.08629180.9970.9990.030.0920.849100
3.09-3.329.60.06829370.99810.0230.0721.035100
3.32-3.669.60.05329360.99910.0180.0561.35199.9
3.66-4.189.30.04629660.99910.0160.0491.73799.8
4.18-5.268.60.04230100.99910.0150.0451.86999.8
5.26-257.20.03131360.99910.0130.0331.46599.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ZAD

8zad


Resolution: 2.45→24.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.012 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.578 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25401 1449 5 %RANDOM
Rwork0.18363 ---
obs0.18727 27799 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.798 Å2
Baniso -1Baniso -2Baniso -3
1--2.96 Å2-0 Å2-0 Å2
2---2.11 Å20 Å2
3---5.06 Å2
Refinement stepCycle: 1 / Resolution: 2.45→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5793 0 2 209 6004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135941
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175423
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.6478024
X-RAY DIFFRACTIONr_angle_other_deg1.2471.57712493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7885703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96921.011366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.657151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8181556
X-RAY DIFFRACTIONr_chiral_restr0.070.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026681
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021431
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_it5.1655.8652827
X-RAY DIFFRACTIONr_mcbond_other5.1525.8622826
X-RAY DIFFRACTIONr_mcangle_it7.3438.7783525
X-RAY DIFFRACTIONr_mcangle_other7.3428.7813526
X-RAY DIFFRACTIONr_scbond_it5.086.2653114
X-RAY DIFFRACTIONr_scbond_other5.086.2683115
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.629.1944500
X-RAY DIFFRACTIONr_long_range_B_refined9.73465.2426923
X-RAY DIFFRACTIONr_long_range_B_other9.73365.2066897
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.506 Å
RfactorNum. reflection% reflection
Rfree0.362 102 -
Rwork0.245 1769 -
obs--86.46 %

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