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- PDB-5dm4: Crystal structure of the plantazolicin methyltransferase BpumL in... -

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Basic information

Entry
Database: PDB / ID: 5dm4
TitleCrystal structure of the plantazolicin methyltransferase BpumL in complex with pentazolic desmethylPZN analog and SAH
ComponentsMethyltransferase domain family
Keywordstransferase/transferase inhibitor / N-methyltransferase / plantazolicin / pentazolic desmethylPZN analog / transferase-transferase inhibitor complex
Function / homologyVaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-5DA / S-ADENOSYL-L-HOMOCYSTEINE / :
Function and homology information
Biological speciesBacillus pumilus ATCC 7061 (bacteria)
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
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase domain family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4164
Polymers30,3861
Non-polymers1,0303
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.813, 78.844, 44.754
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Methyltransferase domain family


Mass: 30385.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus ATCC 7061 (bacteria) / Gene: BAT_2465 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: B4ADV2
#2: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Chemical ChemComp-5DA / 1-[(4S)-4-(4-{4-[4-(5,5'-dimethyl-2,4'-bi-1,3-oxazol-2'-yl)-1,3-thiazol-2-yl]-5-methyl-1,3-oxazol-2-yl}-1,3-thiazol-2-yl)-4-(methylamino)butyl]guanidine


Mass: 553.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C24H27N9O3S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.96 Å3/Da / Density % sol: 37.19 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop
Details: 100mM Bis-tris pH 5.5, 200mM Li2SO4, 22-26% PEG3350

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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: Jul 28, 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: 25053 / % possible obs: 99.96 % / Redundancy: 8 % / Net I/σ(I): 10.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Cootmodel building
PHENIXmodel building
HKL-2000data scaling
RefinementResolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.633 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24303 1270 5.1 %RANDOM
Rwork0.20059 ---
obs0.2027 23630 99.96 %-
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: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.07 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 0 186 2336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192197
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7712.0082972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8685255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56225.1100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5515391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.812158
X-RAY DIFFRACTIONr_chiral_restr0.0780.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211634
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
Rfree0.28 96 -
Rwork0.249 1715 -
obs--100 %

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