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- PDB-5dm0: Crystal structure of the plantazolicin methyltransferase BamL in ... -

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Basic information

Entry
Database: PDB / ID: 5dm0
TitleCrystal structure of the plantazolicin methyltransferase BamL in complex with triazolic desmethylPZN analog and SAH
Componentsplantazolicin methyltransferase BamL
Keywordstransferase/transferase inhibitor / N-methyltransferase / plantazolicin / desmethylPZN analog / 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-5D8 / S-ADENOSYL-L-HOMOCYSTEINE / Class I SAM-dependent methyltransferase
Similarity search - Component
Biological speciesBacillus amyloliquefaciens subsp. plantarum
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 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 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
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
B: plantazolicin methyltransferase BamL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7948
Polymers61,9342
Non-polymers1,8606
Water9,332518
1
A: plantazolicin methyltransferase BamL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8974
Polymers30,9671
Non-polymers9303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: plantazolicin methyltransferase BamL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8974
Polymers30,9671
Non-polymers9303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.839, 96.501, 132.646
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 plantazolicin methyltransferase BamL


Mass: 30966.955 Da / Num. of mol.: 2
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) / Strain (production host): Rosetta 2 / References: UniProt: A7Z2A9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-5D8 / ethyl 2-(2-{2-[(1S)-1-amino-4-carbamimidamidobutyl]-1,3-thiazol-4-yl}-5-methyl-1,3-oxazol-4-yl)-1,3-thiazole-4-carboxylate


Mass: 449.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23N7O3S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100mM Bis-tris, 200mM Li2SO4, 22-26% PEG3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 64060 / % possible obs: 99.48 % / Redundancy: 6.9 % / Net I/σ(I): 6.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
PHENIXmodel building
Cootmodel building
RefinementResolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.142 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21229 3232 5.1 %RANDOM
Rwork0.18582 ---
obs0.18717 60530 99.48 %-
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: 22.276 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 0 122 518 4951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194516
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9716087
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.355536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22724.5220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35315807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1421527
X-RAY DIFFRACTIONr_chiral_restr0.0820.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023391
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 222 -
Rwork0.249 4222 -
obs--95.84 %

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