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- PDB-5tu4: PagF with Boc-Tyr and DMSPP -

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Basic information

Entry
Database: PDB / ID: 5tu4
TitlePagF with Boc-Tyr and DMSPP
ComponentsPagF prenyltransferase
KeywordsTRANSFERASE / RiPP / prenylation / ABBA fold
Function / homologyPeptide O-prenyltransferase, LynF/TruF/PatF family / Family of unknown function (DUF5838) / transferase activity / metal ion binding / N-(tert-butoxycarbonyl)-L-tyrosine / DIMETHYLALLYL S-THIOLODIPHOSPHATE / Putative prenyl transferase
Function and homology information
Biological speciesPlanktothrix agardhii NIES-596 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PagF prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7934
Polymers35,2251
Non-polymers5683
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-12 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.442, 116.442, 43.682
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: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-B1C / N-(tert-butoxycarbonyl)-L-tyrosine / BOC-TYR


Mass: 281.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19NO5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
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: 0.97872 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 19417 / Num. obs: 114490 / % possible obs: 97 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.5
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.673

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.12 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1743 5.07 %RANDOM
Rwork0.184 ---
obs0.187 19016 88.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→38.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 35 199 2702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072562
X-RAY DIFFRACTIONf_angle_d0.9363459
X-RAY DIFFRACTIONf_dihedral_angle_d16.0581520
X-RAY DIFFRACTIONf_chiral_restr0.055364
X-RAY DIFFRACTIONf_plane_restr0.005441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1005-2.16230.3396700.26251786X-RAY DIFFRACTION58
2.1623-2.2320.25681250.24622108X-RAY DIFFRACTION69
2.232-2.31180.32321140.22972382X-RAY DIFFRACTION77
2.3118-2.40440.27671560.23152629X-RAY DIFFRACTION87
2.4044-2.51380.24811540.21952751X-RAY DIFFRACTION91
2.5138-2.64630.32821670.21862915X-RAY DIFFRACTION94
2.6463-2.8120.27131400.20182947X-RAY DIFFRACTION97
2.812-3.0290.24581690.2023000X-RAY DIFFRACTION98
3.029-3.33370.22071790.18543006X-RAY DIFFRACTION99
3.3337-3.81570.18531760.15813004X-RAY DIFFRACTION99
3.8157-4.80590.19171440.1413044X-RAY DIFFRACTION99
4.8059-38.12080.20041490.16413042X-RAY DIFFRACTION99

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