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- PDB-4yl7: Crystal structure of the indole prenyltransferase MpnD from Marin... -

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Basic information

Entry
Database: PDB / ID: 4yl7
TitleCrystal structure of the indole prenyltransferase MpnD from Marinactinospora thermotolerans
ComponentsAromatic prenyltransferase
KeywordsTRANSFERASE / PT-fold / indolactam V / indole prenyltransferase
Function / homologyAromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / Aromatic prenyltransferase
Function and homology information
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 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 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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


Theoretical massNumber of molelcules
Total (without water)41,0271
Polymers41,0271
Non-polymers00
Water6,539363
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.660, 53.700, 132.680
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl (pH8.5), 1470 mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 44641 / % possible obs: 99.6 % / Redundancy: 7.18 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.04
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 6.95 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 5.83 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSXDS-OSX10.9.4_Darwin13.3.0data reduction
XSCALEXDS-OSX10.9.4_Darwin13.3.0data scaling
MOLREPCCP4-6.4.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YZJ

4yzj


Resolution: 1.601→34.139 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 2232 5 %
Rwork0.1801 --
obs0.1813 44640 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.601→34.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 0 363 3154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062871
X-RAY DIFFRACTIONf_angle_d1.1273923
X-RAY DIFFRACTIONf_dihedral_angle_d12.1291032
X-RAY DIFFRACTIONf_chiral_restr0.074414
X-RAY DIFFRACTIONf_plane_restr0.006530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6009-1.63570.29371310.21622508X-RAY DIFFRACTION96
1.6357-1.67380.23971390.19722630X-RAY DIFFRACTION100
1.6738-1.71560.23031360.18712580X-RAY DIFFRACTION100
1.7156-1.7620.22811380.18192624X-RAY DIFFRACTION100
1.762-1.81390.22181390.19292639X-RAY DIFFRACTION100
1.8139-1.87240.26681390.18122639X-RAY DIFFRACTION100
1.8724-1.93930.21531380.1832619X-RAY DIFFRACTION100
1.9393-2.0170.2071380.17172634X-RAY DIFFRACTION100
2.017-2.10880.21631400.16682649X-RAY DIFFRACTION100
2.1088-2.21990.19511400.17272660X-RAY DIFFRACTION100
2.2199-2.3590.21380.17122637X-RAY DIFFRACTION100
2.359-2.5410.21051410.18562671X-RAY DIFFRACTION100
2.541-2.79670.23191400.19292668X-RAY DIFFRACTION100
2.7967-3.20110.2121420.18462689X-RAY DIFFRACTION100
3.2011-4.0320.18611430.16652727X-RAY DIFFRACTION100
4.032-34.14670.16031500.18352834X-RAY DIFFRACTION99

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