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- PDB-6noi: Crystal structure of Tsn15 in apo form -

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Basic information

Entry
Database: PDB / ID: 6noi
TitleCrystal structure of Tsn15 in apo form
ComponentsTsn15
KeywordsLYASE / cyclase / tetronasin
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION
Function and homology information
Biological speciesStreptomyces longisporoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLittle, R. / Paiva, F.C.R. / Dias, M.V.B. / Leadlay, P.
CitationJournal: Nat Catal / Year: 2019
Title: Unexpected enzyme-catalysed [4+2] cycloaddition and rearrangement in polyether antibiotic biosynthesis
Authors: Little, R. / Paiva, F.C.R. / Jenkins, R. / Hong, H. / Sun, Y. / Demydchuk, Y. / Samborskyy, M. / Tosin, M. / Leeper, F.J. / Dias, M.V.B. / Leadlay, P.F.
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Tsn15
B: Tsn15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2086
Polymers45,7622
Non-polymers4464
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-36 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.838, 36.938, 91.815
Angle α, β, γ (deg.)90.000, 107.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tsn15


Mass: 22880.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces longisporoflavus (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M PCTP pH 6, 25% PEG 1500 buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→29.7 Å / Num. obs: 38365 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 15.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Net I/σ(I): 22.7 / Num. measured all: 239481
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.843.90.218786220140.9490.1250.2536.488.7
9-29.75.80.05219823410.9980.0220.05640.696.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.699 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1864 1836 4.79 %
Rwork0.1556 36527 -
obs0.1571 38363 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.41 Å2 / Biso mean: 22.7645 Å2 / Biso min: 7.14 Å2
Refinement stepCycle: final / Resolution: 1.8→29.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 34 407 3587
Biso mean--38.3 35.54 -
Num. residues----412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063338
X-RAY DIFFRACTIONf_angle_d0.8854583
X-RAY DIFFRACTIONf_chiral_restr0.058539
X-RAY DIFFRACTIONf_plane_restr0.005596
X-RAY DIFFRACTIONf_dihedral_angle_d18.6892055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84870.22941360.18572518265489
1.8487-1.90310.22461170.16612737285498
1.9031-1.96450.16481180.153628322950100
1.9645-2.03470.20221590.151228152974100
2.0347-2.11610.2081490.153427722921100
2.1161-2.21240.20381520.15628252977100
2.2124-2.3290.21181510.160728072958100
2.329-2.47490.19751210.163328893010100
2.4749-2.66590.20531410.16728212962100
2.6659-2.93390.20131430.164828292972100
2.9339-3.3580.17781490.156228623011100
3.358-4.22870.15521600.137628543014100
4.2287-29.70310.16541400.152629663106100
Refinement TLS params.Method: refined / Origin x: 24.9135 Å / Origin y: 20.1143 Å / Origin z: 65.6429 Å
111213212223313233
T0.0805 Å2-0.0013 Å2-0.0219 Å2-0.0898 Å2-0.0031 Å2--0.1058 Å2
L0.645 °2-0.0798 °2-0.4746 °2-0.3129 °20.1825 °2--1.4864 °2
S-0.0179 Å °0.0566 Å °-0.0328 Å °-0.0146 Å °0.0066 Å °-0.0166 Å °0.0473 Å °-0 Å °0.0122 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 206
2X-RAY DIFFRACTION1allB3 - 206
3X-RAY DIFFRACTION1allD1 - 2
4X-RAY DIFFRACTION1allE1
5X-RAY DIFFRACTION1allS1 - 407
6X-RAY DIFFRACTION1allC1

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