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- PDB-7fhe: Structure of prenyltransferase mutant Q295F from Streptomyces sp.... -

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Basic information

Entry
Database: PDB / ID: 7fhe
TitleStructure of prenyltransferase mutant Q295F from Streptomyces sp. (strain CL190)
ComponentsPrenyltransferase
KeywordsTRANSFERASE / PT-barrel
Function / homologyAromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metal ion binding / Prenyltransferase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsXue, B. / Lim, K.J.H. / Hartono, Y.D. / Go, M.D.K. / Fan, H. / Yew, W.S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: Acs Catalysis / Year: 2022
Title: Structure-Guided Engineering of Prenyltransferase NphB for High-Yield and Regioselective Cannabinoid Production.
Authors: Lim, K.J.H. / Hartono, Y.D. / Xue, B. / Go, M.K. / Fan, H. / Yew, W.S.
History
DepositionJul 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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: Prenyltransferase


Theoretical massNumber of molelcules
Total (without water)33,9511
Polymers33,9511
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.831, 75.970, 79.508
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Prenyltransferase


Mass: 33951.406 Da / Num. of mol.: 1 / Mutation: Q295F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (strain CL190) (bacteria)
Strain: CL190 / Plasmid: pSY5CDF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4R2T2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 1.95 Å3/Da / Density % sol: 36.91 % / Mosaicity: 0.26 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 18% w/v PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.5→29.45 Å / Num. obs: 9690 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 38.74 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.044 / Rrim(I) all: 0.16 / Net I/σ(I): 11.4 / Num. measured all: 122458 / Scaling rejects: 31
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.015 / Num. unique obs: 1073 / CC1/2: 0.925 / Rpim(I) all: 0.289 / Rrim(I) all: 1.056 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.47 Å29.45 Å
Translation5.47 Å29.45 Å

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZB6

1zb6


Resolution: 2.5→29.45 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2897 444 4.61 %
Rwork0.2053 9190 -
obs0.2092 9634 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.53 Å2 / Biso mean: 42.2289 Å2 / Biso min: 26.86 Å2
Refinement stepCycle: final / Resolution: 2.5→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2266 0 0 5 2271
Biso mean---41.09 -
Num. residues----293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.860.36551430.264229823125
2.86-3.60.3081400.222930573197
3.6-29.450.25911610.179431513312

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