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- PDB-7y9g: Crystal structure of diterpene synthase VenA from Streptomyces ve... -

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Basic information

Entry
Database: PDB / ID: 7y9g
TitleCrystal structure of diterpene synthase VenA from Streptomyces venezuelae ATCC 15439 in complex with pyrophosphate
ComponentsDiterpene synthase VenA
KeywordsLYASE / pyrophosphate / terpenoids
Function / homologyDI(HYDROXYETHYL)ETHER / PYROPHOSPHATE 2-
Function and homology information
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsZhang, L.L. / Xie, Z.Z. / Huang, J.-W. / Hu, Y.C. / Liu, W.D. / Yang, Y. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Molecular insights into the catalytic promiscuity of a bacterial diterpene synthase.
Authors: Li, Z. / Zhang, L. / Xu, K. / Jiang, Y. / Du, J. / Zhang, X. / Meng, L.H. / Wu, Q. / Du, L. / Li, X. / Hu, Y. / Xie, Z. / Jiang, X. / Tang, Y.J. / Wu, R. / Guo, R.T. / Li, S.
History
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diterpene synthase VenA
B: Diterpene synthase VenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,14930
Polymers83,1832
Non-polymers1,96528
Water7,746430
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.789, 92.789, 81.048
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Diterpene synthase VenA


Mass: 41591.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE GENEBANK ACCESSION NUMBER IS QGF19026.1. / Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 7 types, 458 molecules

#2: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG SMEAR MEDIUM; 0.1M HEPES; pH 7.5

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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: Jul 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.18→36.02 Å / Num. obs: 40733 / % possible obs: 99.9 % / Redundancy: 4.49 % / Rmerge(I) obs: 0.0652 / Net I/σ(I): 10.43
Reflection shellResolution: 2.18→2.21 Å / Redundancy: 3.44 % / Rmerge(I) obs: 0.4139 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 1690 / % possible all: 100

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Processing

Software
NameVersionClassification
SAINTdata reduction
SAINTdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TBD

6tbd


Resolution: 2.18→36.02 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.783 / SU ML: 0.167 / SU R Cruickshank DPI: 0.2542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2077 5.3 %RANDOM
Rwork0.1749 ---
obs0.1783 36822 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.27 Å2 / Biso mean: 40.118 Å2 / Biso min: 20.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 2.18→36.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5161 0 118 462 5741
Biso mean--58.74 44.25 -
Num. residues----655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135405
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174920
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.6477252
X-RAY DIFFRACTIONr_angle_other_deg1.3111.57211287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9115652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.23420.272331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11515822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2151559
X-RAY DIFFRACTIONr_chiral_restr0.0720.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021280
LS refinement shellResolution: 2.18→2.237 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 151 -
Rwork0.256 2375 -
all-2526 -
obs--83.73 %

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