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- PDB-7fhd: Structure of prenyltransferase mutant Y288P from Streptomyces sp.... -

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Basic information

Entry
Database: PDB / ID: 7fhd
TitleStructure of prenyltransferase mutant Y288P 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: 3.5 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prenyltransferase
B: Prenyltransferase
C: Prenyltransferase
D: Prenyltransferase


Theoretical massNumber of molelcules
Total (without water)135,4654
Polymers135,4654
Non-polymers00
Water00
1
A: Prenyltransferase


Theoretical massNumber of molelcules
Total (without water)33,8661
Polymers33,8661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prenyltransferase


Theoretical massNumber of molelcules
Total (without water)33,8661
Polymers33,8661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Prenyltransferase


Theoretical massNumber of molelcules
Total (without water)33,8661
Polymers33,8661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Prenyltransferase


Theoretical massNumber of molelcules
Total (without water)33,8661
Polymers33,8661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.2860, 75.1620, 87.6050
Angle α, β, γ (deg.)89.9390, 89.9030, 89.9960
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 41 or resid 46 through 290))
21(chain B and resid 3 through 290)
31(chain C and (resid 3 through 41 or resid 46 through 290))
41(chain D and (resid 3 through 41 or resid 46 through 290))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEU(chain A and (resid 3 through 41 or resid 46 through 290))AA3 - 415 - 43
12SERSERHISHIS(chain A and (resid 3 through 41 or resid 46 through 290))AA46 - 29048 - 292
21GLUGLUHISHIS(chain B and resid 3 through 290)BB3 - 2905 - 292
31GLUGLULEULEU(chain C and (resid 3 through 41 or resid 46 through 290))CC3 - 415 - 43
32SERSERHISHIS(chain C and (resid 3 through 41 or resid 46 through 290))CC46 - 29048 - 292
41GLUGLULEULEU(chain D and (resid 3 through 41 or resid 46 through 290))DD3 - 415 - 43
42SERSERHISHIS(chain D and (resid 3 through 41 or resid 46 through 290))DD46 - 29048 - 292

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Components

#1: Protein
Prenyltransferase


Mass: 33866.305 Da / Num. of mol.: 4 / Mutation: Y288P
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

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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: 2.15 Å3/Da / Density % sol: 42.85 % / Mosaicity: 0.46 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 6% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25% w/v PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3.5→29.2 Å / Num. obs: 13654 / % possible obs: 95.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 41.3 Å2 / CC1/2: 0.914 / Rmerge(I) obs: 0.262 / Rpim(I) all: 0.211 / Rrim(I) all: 0.339 / Net I/σ(I): 2.2 / Num. measured all: 29344
Reflection shellResolution: 3.5→3.83 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.446 / Num. unique obs: 3344 / CC1/2: 0.797 / Rpim(I) all: 0.362 / Rrim(I) all: 0.578 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å29.2 Å
Translation3.2 Å29.2 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: 3.5→29.2 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 30.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.313 764 5.6 %
Rwork0.2426 12881 -
obs0.2466 13645 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.03 Å2 / Biso mean: 29.0734 Å2 / Biso min: 3.02 Å2
Refinement stepCycle: final / Resolution: 3.5→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8673 0 0 0 8673
Num. residues----1121
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5238X-RAY DIFFRACTION11.761TORSIONAL
12B5238X-RAY DIFFRACTION11.761TORSIONAL
13C5238X-RAY DIFFRACTION11.761TORSIONAL
14D5238X-RAY DIFFRACTION11.761TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.770.29261530.24042645279898
3.77-4.150.36021480.24662617276597
4.15-4.750.2871990.23972475267495
4.75-5.970.29721500.26142544269495
5.97-29.20.34991140.22822600271495

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