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- PDB-8zaf: Crystal structure of SkABA3 from Shimazuella kribbensis -

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Basic information

Entry
Database: PDB / ID: 8zaf
TitleCrystal structure of SkABA3 from Shimazuella kribbensis
ComponentsSesquiterpene synthases
KeywordsLYASE / SkABA3 / Sesquiterpene synthases / apo-form
Biological speciesShimazuella kribbensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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: Sesquiterpene synthases
B: Sesquiterpene synthases
C: Sesquiterpene synthases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,17210
Polymers140,5923
Non-polymers5807
Water11,890660
1
A: Sesquiterpene synthases
B: Sesquiterpene synthases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2438
Polymers93,7282
Non-polymers5156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-85 kcal/mol
Surface area27540 Å2
MethodPISA
2
C: Sesquiterpene synthases
hetero molecules

C: Sesquiterpene synthases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8594
Polymers93,7282
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4140 Å2
ΔGint-25 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.216, 107.800, 81.529
Angle α, β, γ (deg.)90.00, 103.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sesquiterpene synthases


Mass: 46863.992 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shimazuella kribbensis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / 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

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Magnesium chloride, 0.1 M Bis-Tris pH 6.5, 1.4 M Ammonium sulfate

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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: Sep 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.96→25 Å / Num. obs: 130215 / % possible obs: 97.9 % / Redundancy: 3.6 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.025 / Rrim(I) all: 0.048 / Χ2: 1.052 / Net I/σ(I): 18.9 / Num. measured all: 470351
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.96-2.033.30.588127290.8930.9710.3620.6950.51196.4
2.03-2.113.60.414130180.9540.9880.2460.4840.93397.9
2.11-2.2140.249132110.9810.9950.1370.2850.65299.6
2.21-2.323.30.224122740.9710.9930.1420.2671.7792.7
2.32-2.4740.096132300.9950.9990.0550.1110.8399.6
2.47-2.663.60.067132190.9960.9990.040.0781.0899.6
2.66-2.933.80.052132140.9970.9990.0310.0611.24699.3
2.93-3.353.80.036132200.99810.0210.0421.37499.6
3.35-4.223.50.029127290.99810.0180.0341.16795.2
4.22-253.30.022133710.99910.0140.0271.06998.9

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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: 1.96→24.87 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.214 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22322 6466 5 %RANDOM
Rwork0.19601 ---
obs0.1974 122812 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.671 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å20.71 Å2
2---1.56 Å2-0 Å2
3----2.2 Å2
Refinement stepCycle: 1 / Resolution: 1.96→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8393 0 23 660 9076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0138589
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177868
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.64711620
X-RAY DIFFRACTIONr_angle_other_deg1.4321.57118179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71551022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24621.369504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.937151500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.951574
X-RAY DIFFRACTIONr_chiral_restr0.0890.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021952
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_it4.3084.3274112
X-RAY DIFFRACTIONr_mcbond_other4.3084.3264111
X-RAY DIFFRACTIONr_mcangle_it5.8866.4615126
X-RAY DIFFRACTIONr_mcangle_other5.8856.4635127
X-RAY DIFFRACTIONr_scbond_it5.2014.8884477
X-RAY DIFFRACTIONr_scbond_other5.24.8854475
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7447.0936494
X-RAY DIFFRACTIONr_long_range_B_refined9.46150.34810106
X-RAY DIFFRACTIONr_long_range_B_other9.462509982
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.007 Å
RfactorNum. reflection% reflection
Rfree0.274 405 -
Rwork0.292 8751 -
obs--93.37 %

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