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- PDB-8zae: Crystal structure of RuABA3 from Rutstroemia sp. NJR-2017a WRK4 i... -

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Basic information

Entry
Database: PDB / ID: 8zae
TitleCrystal structure of RuABA3 from Rutstroemia sp. NJR-2017a WRK4 in complex with FsPP
ComponentsAba 3 protein
KeywordsLYASE / RuABA3 / Sesquiterpene synthases / FsPP
Function / homologyChem-FPS / Aba 3 protein
Function and homology information
Biological speciesRutstroemia sp. NJR-2017a WRK4 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 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: Aba 3 protein
B: Aba 3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4948
Polymers93,5182
Non-polymers9766
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-62 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.765, 89.475, 142.712
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 Aba 3 protein


Mass: 46758.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rutstroemia sp. NJR-2017a WRK4 (fungus)
Gene: CJF32_00009727 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S7P8J3
#2: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 0.2 M sodium malonate pH 7.0, 21% PEG 3350, 0.1 M Bis-Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Aug 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.28→35.03 Å / Num. obs: 27175 / % possible obs: 98.1 % / Redundancy: 7.3 % / CC1/2: 0.996 / Net I/σ(I): 8.5
Reflection shellResolution: 2.28→2.32 Å / Num. unique obs: 1746 / CC1/2: 0.792

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Processing

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

8zad


Resolution: 2.28→35.03 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.548 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.515 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25018 1444 5 %RANDOM
Rwork0.17689 ---
obs0.18057 27175 93.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.589 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å2-0 Å2
2---2.15 Å20 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 2.28→35.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5451 0 52 317 5820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135628
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175152
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.657612
X-RAY DIFFRACTIONr_angle_other_deg1.2921.57311855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8585663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48120.576347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59715934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8861554
X-RAY DIFFRACTIONr_chiral_restr0.0740.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021366
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_it3.1383.7242670
X-RAY DIFFRACTIONr_mcbond_other3.1313.7232669
X-RAY DIFFRACTIONr_mcangle_it4.7265.5673327
X-RAY DIFFRACTIONr_mcangle_other4.7265.5683328
X-RAY DIFFRACTIONr_scbond_it3.3484.052958
X-RAY DIFFRACTIONr_scbond_other3.3354.0442952
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2015.9364286
X-RAY DIFFRACTIONr_long_range_B_refined6.98842.1296651
X-RAY DIFFRACTIONr_long_range_B_other6.98542.0666621
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 103 -
Rwork0.273 1746 -
obs--82.88 %

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