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- PDB-4yla: Crystal structure of the indole prenyltransferase MpnD complexed ... -

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Basic information

Entry
Database: PDB / ID: 4yla
TitleCrystal structure of the indole prenyltransferase MpnD complexed with indolactam V and DMSPP
ComponentsAromatic prenyltransferase
KeywordsTRANSFERASE / indole prenyltransferase / PT-fold / indolactam V
Function / homologyAromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / DIMETHYLALLYL S-THIOLODIPHOSPHATE / Chem-ILV / Aromatic prenyltransferase
Function and homology information
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMori, T. / Morita, H. / Abe, I.
CitationJournal: Nat Commun / Year: 2016
Title: Manipulation of prenylation reactions by structure-based engineering of bacterial indolactam prenyltransferases.
Authors: Mori, T. / Zhang, L. / Awakawa, T. / Hoshino, S. / Okada, M. / Morita, H. / Abe, I.
History
DepositionMar 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 2.0Oct 16, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_struct_oper_list
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8796
Polymers41,0271
Non-polymers8525
Water7,728429
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.830, 54.080, 132.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aromatic prenyltransferase


Mass: 41027.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinactinospora thermotolerans (bacteria)
Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: I7EIW6
#2: Chemical ChemComp-ILV / (2S,5S)-5-(hydroxymethyl)-1-methyl-2-(propan-2-yl)-1,2,4,5,6,8-hexahydro-3H-[1,4]diazonino[7,6,5-cd]indol-3-one / Indolactam V


Mass: 301.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N3O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate / Dimethylallyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl (pH8.5), 1470 mM (NH)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 66872 / % possible obs: 99.7 % / Redundancy: 6.98 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.83
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.03 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSXDS-OSX10.9.4_Darwin13.3.0data reduction
XSCALEOSX10.9.4_Darwin13.3.0data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YZJ

4yzj


Resolution: 1.4→41.861 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 3344 5 %
Rwork0.1778 --
obs0.1791 66871 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→41.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 51 429 3296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092946
X-RAY DIFFRACTIONf_angle_d1.2474031
X-RAY DIFFRACTIONf_dihedral_angle_d13.0581081
X-RAY DIFFRACTIONf_chiral_restr0.076424
X-RAY DIFFRACTIONf_plane_restr0.007541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3998-1.41980.2891360.23912581X-RAY DIFFRACTION97
1.4198-1.4410.26461350.22112572X-RAY DIFFRACTION100
1.441-1.46360.22961410.21052670X-RAY DIFFRACTION100
1.4636-1.48760.22451350.20622578X-RAY DIFFRACTION100
1.4876-1.51320.23231380.19342616X-RAY DIFFRACTION100
1.5132-1.54070.23331380.19582617X-RAY DIFFRACTION100
1.5407-1.57040.21721380.18362627X-RAY DIFFRACTION100
1.5704-1.60240.2341380.17672613X-RAY DIFFRACTION100
1.6024-1.63730.19551390.18462655X-RAY DIFFRACTION100
1.6373-1.67530.20211390.18632633X-RAY DIFFRACTION100
1.6753-1.71720.2161360.18142589X-RAY DIFFRACTION100
1.7172-1.76370.22191390.17962639X-RAY DIFFRACTION100
1.7637-1.81560.20821390.17992642X-RAY DIFFRACTION100
1.8156-1.87420.22481400.17412662X-RAY DIFFRACTION100
1.8742-1.94120.19241390.17872637X-RAY DIFFRACTION100
1.9412-2.01890.20781380.17642619X-RAY DIFFRACTION100
2.0189-2.11080.2081410.17042677X-RAY DIFFRACTION100
2.1108-2.2220.18291390.16642653X-RAY DIFFRACTION100
2.222-2.36120.21271400.17082658X-RAY DIFFRACTION100
2.3612-2.54350.18241410.17492667X-RAY DIFFRACTION100
2.5435-2.79950.20561420.18562700X-RAY DIFFRACTION100
2.7995-3.20440.18381420.17652696X-RAY DIFFRACTION100
3.2044-4.03670.19361430.15992731X-RAY DIFFRACTION100
4.0367-41.880.19441480.18072795X-RAY DIFFRACTION97

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