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- PDB-7fhb: Structure of prenyltransferase from Streptomyces sp. (strain CL19... -

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Basic information

Entry
Database: PDB / ID: 7fhb
TitleStructure of prenyltransferase from Streptomyces sp. (strain CL190) with bound GPP
ComponentsPrenyltransferase
KeywordsTRANSFERASE / PT-barrel
Function / homologyAromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metal ion binding / GERANYL DIPHOSPHATE / Prenyltransferase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2472
Polymers33,9321
Non-polymers3141
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint2 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.462, 78.360, 84.992
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: 33932.363 Da / Num. of mol.: 1
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: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.62 %
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: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 23861 / % possible obs: 98.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.79 Å2 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.051 / Rrim(I) all: 0.132 / Χ2: 0.912 / Net I/σ(I): 9.2 / Num. measured all: 156859
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9350.710770.4650.3350.780.75689.2
1.93-1.975.30.66710750.8040.3070.7370.80892.6
1.97-2.015.50.5511610.9170.250.6070.80897.4
2.01-2.055.80.54711790.8970.2430.6010.79899.4
2.05-2.096.20.45911760.9410.20.5020.84399.8
2.09-2.146.60.40311980.9440.170.4380.843100
2.14-2.196.80.36711720.9640.1510.3970.91100
2.19-2.2570.33111940.9670.1350.3580.951100
2.25-2.3270.28511970.9770.1160.3080.951100
2.32-2.3970.24611840.9810.10.2660.947100
2.39-2.487.10.2212070.9870.090.2380.945100
2.48-2.587.10.1911900.9860.0770.2050.917100
2.58-2.77.10.15711990.9890.0640.1690.903100
2.7-2.8470.12912110.9880.0530.140.90999.9
2.84-3.027.10.10712090.9930.0440.1160.86100
3.02-3.2570.09612080.9910.040.1040.935100
3.25-3.576.90.09612070.9810.0410.1051.13699.6
3.57-4.096.70.07912440.9820.0340.0870.97199.1
4.09-5.156.50.05512290.9920.0240.060.71699.3
5.15-306.60.07313440.9930.030.0791.153100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.8 Å29.4 Å
Translation5.8 Å29.4 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.8.3phasing
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZB6

1zb6


Resolution: 1.9→29.4 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 1748 5.04 %
Rwork0.1763 20537 -
obs0.1786 21627 89.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.05 Å2 / Biso mean: 20.7619 Å2 / Biso min: 10.37 Å2
Refinement stepCycle: final / Resolution: 1.9→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 19 288 2669
Biso mean--31.38 29.54 -
Num. residues----306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.990.3032840.22481675175960
1.99-2.090.24811130.18672067218073
2.09-2.220.21731230.18142471259488
2.22-2.390.24391430.18022762290598
2.39-2.630.24911700.187128272997100
2.63-3.020.24261410.178228633004100
3.02-3.80.19061450.16272867301299
3.8-29.40.20421710.1713005317699

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