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- PDB-5inj: Crystal Structure of Prenyltransferase PriB Ternary Complex with ... -

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Basic information

Entry
Database: PDB / ID: 5inj
TitleCrystal Structure of Prenyltransferase PriB Ternary Complex with L-Tryptophan and Dimethylallyl thiolodiphosphate (DMSPP)
ComponentsPrenyltransferase
KeywordsTRANSFERASE / Prenyltransferase / tryptophan / DMSPP / indole-PT / ABBA family / PT fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homologyAromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / DIMETHYLALLYL S-THIOLODIPHOSPHATE / TRYPTOPHAN / Prenyltransferase
Function and homology information
Biological speciesStreptomyces sp. RM-5-8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.4 Å
AuthorsCao, H. / Elshahawi, S. / Benach, J. / Wasserman, S.R. / Morisco, L.L. / Koss, J.W. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098248 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA84374 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR000117 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Structure and specificity of a permissive bacterial C-prenyltransferase.
Authors: Elshahawi, S.I. / Cao, H. / Shaaban, K.A. / Ponomareva, L.V. / Subramanian, T. / Farman, M.L. / Spielmann, H.P. / Phillips, G.N. / Thorson, J.S. / Singh, S.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Mar 29, 2017Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 23, 2020Group: Structure summary / Category: audit_author / chem_comp / Item: _audit_author.name / _chem_comp.pdbx_synonyms
Revision 2.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9894
Polymers43,4011
Non-polymers5893
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.396, 83.422, 41.618
Angle α, β, γ (deg.)90.000, 106.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Prenyltransferase / PriB


Mass: 43400.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. RM-5-8 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A182DWE5*PLUS
#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PriB was crystallized by sitting drop vapor diffusion method by 1:1 v/v mixing of 10 mg/mL PriB solution in the presence of 1 mM L-Tryptophan with reservoir solution containing 0.1 M Tris pH ...Details: PriB was crystallized by sitting drop vapor diffusion method by 1:1 v/v mixing of 10 mg/mL PriB solution in the presence of 1 mM L-Tryptophan with reservoir solution containing 0.1 M Tris pH 8.5, 20% w/v PEG 3350, 0.1 M MgCl2. The mixed drops of 0.4-1 uL were equilibrated over a reservoir solution of 50 uL and incubated at 20oC in the dark. The ternary complex was obtained by 1:1.5 v/v soaking a solution of substrate mimic 25 mM Dimethylallyl S-thiolodiphosphate (DMSAPP), 0.05 M Tris pH 8.5, 10% w/v PEG 3350, 0.05 M MgCl2 into PriB crystals. The iodine derivative was prepared by 1:3 v/v soaking a solution of 0.5 M sodium iodide, 0.05 M Tris pH 8.5, 10% w/v PEG 3350, 0.05 M MgCl2 into PriB crystals

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.186→28.82 Å / Num. obs: 65094 / % possible obs: 96.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.098 / Rsym value: 0.075 / Net I/av σ(I): 5.953 / Net I/σ(I): 6.6 / Num. measured all: 229158
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.4-1.482.90.6561.2187.2
1.48-1.573.60.4771.6196.7
1.57-1.673.60.2982.6197.1
1.67-1.813.60.1874.1197.4
1.81-1.983.60.1245.8197.9
1.98-2.213.60.0887.5198.2
2.21-2.563.60.0749198.5
2.56-3.133.60.0797.3198.9
3.13-4.433.60.04812199.1
4.43-28.823.50.04114.9196

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.2.5data scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→28.816 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.53
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2000 3.07 %Random Selection
Rwork0.162 ---
obs0.163 65074 96.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.71 Å2 / Biso mean: 23.3976 Å2 / Biso min: 7.6 Å2
Refinement stepCycle: final / Resolution: 1.4→28.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 70 532 3283
Biso mean--26.69 34.31 -
Num. residues----355
LS refinement shellResolution: 1.4→1.435 Å
RfactorNum. reflection% reflection
Rfree0.349 118 -
Rwork0.3283 3736 -
obs--79 %

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