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

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Basic information

Entry
Database: PDB / ID: 8zad
TitleCrystal structure of RuABA3 from Rutstroemia sp. NJR-2017a WRK4
ComponentsAba 3 protein
KeywordsLYASE / RuABA3 / Sesquiterpene synthases / apo-form
Function / homologyAba 3 protein
Function and homology information
Biological speciesRutstroemia sp. NJR-2017a WRK4 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aba 3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8242
Polymers46,7591
Non-polymers651
Water6,756375
1
A: Aba 3 protein
hetero molecules

A: Aba 3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6494
Polymers93,5182
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4620 Å2
ΔGint-38 kcal/mol
Surface area26100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.324, 141.011, 90.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-867-

HOH

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Components

#1: Protein Aba 3 protein


Mass: 46758.855 Da / Num. of mol.: 1
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 8000, 0.1 M CAPS pH 10.5, 0.2 M NaCl

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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: Sep 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.1→36.39 Å / Num. obs: 25866 / % possible obs: 99.9 % / Redundancy: 7.62 % / CC1/2: 0.996 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.13 Å / Num. unique obs: 1045 / 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: AlphaFold

Resolution: 2.1→36.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.385 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21166 1308 5.1 %RANDOM
Rwork0.16388 ---
obs0.16631 24504 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.186 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å2-0 Å20 Å2
2---1.13 Å20 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.1→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 1 375 3174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132879
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172618
X-RAY DIFFRACTIONr_angle_refined_deg1.61.6473896
X-RAY DIFFRACTIONr_angle_other_deg1.4251.5746023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68520.791177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15615479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2391528
X-RAY DIFFRACTIONr_chiral_restr0.0840.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
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_it1.9492.2271379
X-RAY DIFFRACTIONr_mcbond_other1.9442.2251378
X-RAY DIFFRACTIONr_mcangle_it3.0063.3291722
X-RAY DIFFRACTIONr_mcangle_other3.0083.3321723
X-RAY DIFFRACTIONr_scbond_it2.6762.5091499
X-RAY DIFFRACTIONr_scbond_other2.6752.5111500
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2113.6462175
X-RAY DIFFRACTIONr_long_range_B_refined5.91926.7623588
X-RAY DIFFRACTIONr_long_range_B_other5.74926.2013499
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 99 -
Rwork0.22 1755 -
obs--99.2 %

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