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- PDB-8qnf: Crystal structure of the Condensation domain TomBC from the Tomay... -

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Basic information

Entry
Database: PDB / ID: 8qnf
TitleCrystal structure of the Condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase
ComponentsCondensation domain TomBC from the Tomaymycin 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: 1.65 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
DepositionSep 26, 2023Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,22123
Polymers59,2911
Non-polymers93022
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-72 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.650, 160.060, 163.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-355-

ARG

21A-887-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase


Mass: 59291.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TomBC / Source: (gene. exp.) Streptomyces regensis (bacteria) / Variant: FH6421 / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 382 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Protein (stored in 50mM Kpi, 150 mM NaCl, pH 7.0) crystallised at 30mg/mL at 4 degC in 100 mM Tris pH 8.5, 3.5 M NaFormate 25% glycerol used as cryoprotectant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.65→19.94 Å / Num. obs: 81329 / % possible obs: 85 % / Redundancy: 4.9 % / Biso Wilson estimate: 30.63 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.43
Reflection shellResolution: 1.65→1.7 Å / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2759 / CC1/2: 0.694

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→19.94 Å / SU ML: 0.1726 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5679
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 4067 5 %
Rwork0.1771 77257 -
obs0.1781 81324 85.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.34 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 54 360 3888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513891
X-RAY DIFFRACTIONf_angle_d1.4185314
X-RAY DIFFRACTIONf_chiral_restr0.0763583
X-RAY DIFFRACTIONf_plane_restr0.0144731
X-RAY DIFFRACTIONf_dihedral_angle_d6.5026576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.3344260.3097502X-RAY DIFFRACTION16.33
1.67-1.690.2597520.2772973X-RAY DIFFRACTION31.52
1.69-1.710.3386680.28141300X-RAY DIFFRACTION42
1.71-1.730.3157820.28861547X-RAY DIFFRACTION49.91
1.73-1.760.3089960.28781823X-RAY DIFFRACTION58.52
1.76-1.780.29791060.28872029X-RAY DIFFRACTION65.98
1.78-1.810.34021190.31732247X-RAY DIFFRACTION72.96
1.81-1.840.31761310.30432498X-RAY DIFFRACTION80.2
1.84-1.870.32751430.29062711X-RAY DIFFRACTION87.25
1.87-1.90.22691530.25432918X-RAY DIFFRACTION93.6
1.9-1.930.29031590.24233020X-RAY DIFFRACTION98
1.93-1.970.22361610.22773055X-RAY DIFFRACTION98.14
1.97-2.010.25091620.21883068X-RAY DIFFRACTION98.42
2.01-2.060.21581590.20393039X-RAY DIFFRACTION98.52
2.06-2.10.24161610.20863046X-RAY DIFFRACTION98.22
2.1-2.160.20871620.18883073X-RAY DIFFRACTION98.78
2.16-2.210.22781610.18113075X-RAY DIFFRACTION98.75
2.21-2.280.20281600.17813037X-RAY DIFFRACTION97.26
2.28-2.350.21111620.17323077X-RAY DIFFRACTION98.96
2.35-2.440.19981630.17633095X-RAY DIFFRACTION98.79
2.44-2.530.18861620.17993071X-RAY DIFFRACTION98.66
2.53-2.650.1931620.18653089X-RAY DIFFRACTION98.9
2.65-2.790.22821640.18213105X-RAY DIFFRACTION99
2.79-2.960.19631620.18633077X-RAY DIFFRACTION98.45
2.96-3.190.2021640.18043115X-RAY DIFFRACTION99.48
3.19-3.510.17241650.16363140X-RAY DIFFRACTION99.67
3.51-4.010.15561650.13673140X-RAY DIFFRACTION99.46
4.01-5.040.15611660.13023159X-RAY DIFFRACTION98.99
5.05-19.940.19371710.18633228X-RAY DIFFRACTION98.58

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