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- PDB-5dly: Crystal structure of the plantazolicin methyltransferase BamL in ... -

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Basic information

Entry
Database: PDB / ID: 5dly
TitleCrystal structure of the plantazolicin methyltransferase BamL in complex with monoazolic desmethylPZN analog and SAH
Componentsplantazolicin methyltransferase BamL
Keywordstransferase/transferase inhibitor / plantazolicin / N-methyltransferase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5D7 / S-ADENOSYL-L-HOMOCYSTEINE / Class I SAM-dependent methyltransferase
Similarity search - Component
Biological speciesBacillus amyloliquefaciens subsp. plantarum
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsHao, Y. / Nair, S.K.
CitationJournal: ACS Chem. Biol. / Year: 2015
Title: Insights into methyltransferase specificity and bioactivity of derivatives of the antibiotic plantazolicin.
Authors: Hao, Y. / Blair, P.M. / Sharma, A. / Mitchell, D.A. / Nair, S.K.
History
DepositionSep 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 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

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Assembly

Deposited unit
A: plantazolicin methyltransferase BamL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0143
Polymers30,3321
Non-polymers6822
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.700, 71.370, 48.790
Angle α, β, γ (deg.)90.00, 107.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein plantazolicin methyltransferase BamL


Mass: 30332.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens subsp. plantarum (strain DSM 23117 / BGSC 10A6 / FZB42) (bacteria)
Strain: DSM 23117 / BGSC 10A6 / FZB42 / Gene: RBAM_007500 / Production host: Escherichia coli (E. coli) / References: UniProt: A7Z2A9
#2: Chemical ChemComp-5D7 / prop-2-en-1-yl 2-[(1S)-1-amino-4-carbamimidamidobutyl]-1,3-thiazole-4-carboxylate


Mass: 297.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H19N5O2S
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM Bis-Tris propane, pH 5.5, 200 mM Li2SO4, and 22-26% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 40012 / % possible obs: 96.1 % / Redundancy: 5.3 % / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XSCALEdata scaling
PHENIXphasing
Cootmodel building
RefinementResolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.574 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23695 2001 5 %RANDOM
Rwork0.20638 ---
obs0.2079 38011 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.363 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å2-0.35 Å2
2--1.68 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2179 0 0 237 2416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192219
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9632987
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0025265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38224.587109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97515401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6951513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021662
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 143 -
Rwork0.286 2718 -
obs--93.04 %

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