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- PDB-8rz6: SeMet derivative structure of the condensation domain TomBC from ... -

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Basic information

Entry
Database: PDB / ID: 8rz6
TitleSeMet derivative structure of the condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase
ComponentsTomaymycin non-ribosomal peptide synthetase
KeywordsBIOSYNTHETIC PROTEIN / Non-ribosomal peptide synthetase / Tomaymycin / Condensation
Function / homologyFORMIC ACID / :
Function and homology information
Biological speciesStreptomyces regensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKaranth, M. / Schmelz, S. / Kirkpatrick, J. / Krausze, J. / Scrima, A. / Carlomagno, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG CA294/16-1 Germany
CitationJournal: Sci Adv / Year: 2024
Title: The specificity of intermodular recognition in a prototypical nonribosomal peptide synthetase depends on an adaptor domain.
Authors: Karanth, M.N. / Kirkpatrick, J.P. / Krausze, J. / Schmelz, S. / Scrima, A. / Carlomagno, T.
History
DepositionFeb 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tomaymycin non-ribosomal peptide synthetase
B: Tomaymycin non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,04313
Polymers119,4262
Non-polymers61711
Water10,557586
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.350, 160.870, 100.150
Angle α, β, γ (deg.)90.00, 125.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tomaymycin non-ribosomal peptide synthetase


Mass: 59713.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SeMet derivative structure of the condensation domain TomBC from Tomaymycin non-ribosomal peptide synthetase
Source: (gene. exp.) Streptomyces regensis (bacteria) / Variant: FH6421 / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.43 Å3/Da / Density % sol: 64.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris pH 8.5, 3.0 M KFormate, with 25% glycerol used as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979733 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979733 Å / Relative weight: 1
ReflectionResolution: 2.3→48.91 Å / Num. obs: 139112 / % possible obs: 99.1 % / Redundancy: 10.58 % / CC1/2: 0.994 / Net I/σ(I): 9.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 10.82 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 16569 / CC1/2: 0.747 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
AutoSolphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→48.91 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 3515 5 %
Rwork0.1724 --
obs0.1746 70285 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6825 0 34 586 7445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117084
X-RAY DIFFRACTIONf_angle_d1.0119648
X-RAY DIFFRACTIONf_dihedral_angle_d5.8451007
X-RAY DIFFRACTIONf_chiral_restr0.0531080
X-RAY DIFFRACTIONf_plane_restr0.0111294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.29431380.23412623X-RAY DIFFRACTION99
2.33-2.360.29121390.22762637X-RAY DIFFRACTION99
2.36-2.40.22591400.20882668X-RAY DIFFRACTION99
2.4-2.440.24991390.2082649X-RAY DIFFRACTION99
2.44-2.480.27191390.20992637X-RAY DIFFRACTION99
2.48-2.520.26411410.19882670X-RAY DIFFRACTION99
2.52-2.570.23891400.20452669X-RAY DIFFRACTION99
2.57-2.620.30141400.20582649X-RAY DIFFRACTION99
2.62-2.670.2471400.1992664X-RAY DIFFRACTION99
2.67-2.730.23951410.19212680X-RAY DIFFRACTION99
2.73-2.790.2411390.18252647X-RAY DIFFRACTION99
2.79-2.860.23681410.18142669X-RAY DIFFRACTION99
2.86-2.940.25631400.18312663X-RAY DIFFRACTION99
2.94-3.020.24011410.19432680X-RAY DIFFRACTION99
3.02-3.120.23911400.18662665X-RAY DIFFRACTION100
3.12-3.230.24151410.18892669X-RAY DIFFRACTION100
3.23-3.360.20971410.16882682X-RAY DIFFRACTION100
3.36-3.520.18621410.15422679X-RAY DIFFRACTION100
3.52-3.70.18841410.14892676X-RAY DIFFRACTION100
3.7-3.930.18591410.14832686X-RAY DIFFRACTION100
3.93-4.240.18121410.13582683X-RAY DIFFRACTION100
4.24-4.660.16411410.12532678X-RAY DIFFRACTION100
4.66-5.330.17391430.13112716X-RAY DIFFRACTION100
5.34-6.720.23111430.18922711X-RAY DIFFRACTION100
6.72-100.22431440.20442720X-RAY DIFFRACTION99

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