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- PDB-5tu5: PagF prenyltransferase with Tyr-Tyr-Tyr and DMSPP -

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Basic information

Entry
Database: PDB / ID: 5tu5
TitlePagF prenyltransferase with Tyr-Tyr-Tyr and DMSPP
Components
  • PagF prenyltransferase
  • TYR-TYR-TYR
KeywordsTRANSFERASE / RiPP / prenylation / ABBA fold
Function / homologyPeptide O-prenyltransferase, LynF/TruF/PatF family / Family of unknown function (DUF5838) / transferase activity / metal ion binding / DIMETHYLALLYL S-THIOLODIPHOSPHATE / Putative prenyl transferase
Function and homology information
Biological speciesPlanktothrix agardhii NIES-596 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHao, Y. / Nair, S.K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Molecular basis for the broad substrate selectivity of a peptide prenyltransferase.
Authors: Hao, Y. / Pierce, E. / Roe, D. / Morita, M. / McIntosh, J.A. / Agarwal, V. / Cheatham, T.E. / Schmidt, E.W. / Nair, S.K.
History
DepositionNov 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Derived calculations
Revision 1.2Dec 21, 2016Group: Database references
Revision 2.0Oct 2, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PagF prenyltransferase
B: TYR-TYR-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0194
Polymers35,7332
Non-polymers2862
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-17 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.042, 117.042, 43.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PagF prenyltransferase


Mass: 35224.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planktothrix agardhii NIES-596 (bacteria)
Gene: pagF / Production host: Escherichia coli (E. coli) / References: UniProt: F5B6Z0
#2: Protein/peptide TYR-TYR-TYR


Mass: 507.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / Details: 20-25% PEG 3350 20 mM Tris-HCl pH=7.5 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 27191 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rsym value: 0.091 / Net I/σ(I): 15.6
Reflection shellResolution: 1.9→1.93 Å / Rsym value: 0.675

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.56 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23055 1353 5 %RANDOM
Rwork0.2073 ---
obs0.20845 25660 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.843 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å2-0 Å2
2--0.07 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 15 136 2655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192580
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.9543482
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6575298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21924.672137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66515454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2391510
X-RAY DIFFRACTIONr_chiral_restr0.0890.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021966
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4062.1851198
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5763.2691494
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2342.2531382
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.38129.4563962
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 96 -
Rwork0.268 1693 -
obs--89.99 %

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