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- PDB-6ec7: Glutamylation domain, TbtB, from thiomuracin biosynthesis -

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Basic information

Entry
Database: PDB / ID: 6ec7
TitleGlutamylation domain, TbtB, from thiomuracin biosynthesis
ComponentsLantibiotic dehydratase domain protein
KeywordsBIOSYNTHETIC PROTEIN / RiPP / thiopeptide / thiomuracin / tRNA-dependent / glutamylation / dehydratase
Function / homologyLantibiotic dehydratase, N-terminal / Lantibiotic dehydratase, N terminus / Lantibiotic dehydratase domain protein
Function and homology information
Biological speciesThermobispora bispora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsCogan, D.P. / Nair, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Characterization of glutamyl-tRNA-dependent dehydratases using nonreactive substrate mimics.
Authors: Bothwell, I.R. / Cogan, D.P. / Kim, T. / Reinhardt, C.J. / van der Donk, W.A. / Nair, S.K.
History
DepositionAug 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lantibiotic dehydratase domain protein


Theoretical massNumber of molelcules
Total (without water)96,0071
Polymers96,0071
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.819, 96.406, 107.013
Angle α, β, γ (deg.)90.00, 98.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lantibiotic dehydratase domain protein


Mass: 96006.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51) (bacteria)
Strain: ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51
Gene: Tbis_0550 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6Y502
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M ammonium citrate pH 7.0, 15% PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.151→105.764 Å / Num. obs: 48860 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.028 / Net I/σ(I): 15.1
Reflection shellResolution: 2.151→2.188 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2405 / CC1/2: 0.893 / Rpim(I) all: 0.265 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
autoPROCdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→105.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.955 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27657 2496 5.1 %RANDOM
Rwork0.21379 ---
obs0.21704 46363 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.606 Å2
Baniso -1Baniso -2Baniso -3
1-4.6 Å2-0 Å2-1.64 Å2
2---1.16 Å20 Å2
3----2.8 Å2
Refinement stepCycle: 1 / Resolution: 2.15→105.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6239 0 0 230 6469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196484
X-RAY DIFFRACTIONr_bond_other_d0.0020.026297
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.9768821
X-RAY DIFFRACTIONr_angle_other_deg1.062314436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8835804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30720.756291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46151046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7531599
X-RAY DIFFRACTIONr_chiral_restr0.1060.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217204
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021443
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_it4.1344.8373225
X-RAY DIFFRACTIONr_mcbond_other4.1354.8373224
X-RAY DIFFRACTIONr_mcangle_it6.1857.244026
X-RAY DIFFRACTIONr_mcangle_other6.1857.244027
X-RAY DIFFRACTIONr_scbond_it4.4175.3253259
X-RAY DIFFRACTIONr_scbond_other4.4175.3253260
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7187.84796
X-RAY DIFFRACTIONr_long_range_B_refined9.6158.1327147
X-RAY DIFFRACTIONr_long_range_B_other9.61558.0927125
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 167 -
Rwork0.307 3398 -
obs--99.97 %

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