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- PDB-6t6x: Structure of the Bottromycin epimerase BotH in complex with substrate -

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Basic information

Entry
Database: PDB / ID: 6t6x
TitleStructure of the Bottromycin epimerase BotH in complex with substrate
ComponentsBotH
KeywordsHYDROLASE / Bottromycin / RiPP / Epimerase / ABH
Function / homologyalpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / metal ion binding / Chem-MQW / BotH
Function and homology information
Biological speciesStreptomyces sp. BC16019 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKoehnke, J. / Sikandar, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationKO 4116/3-1 Germany
Citation
Journal: Nat.Chem.Biol. / Year: 2020
Title: The bottromycin epimerase BotH defines a group of atypical alpha / beta-hydrolase-fold enzymes.
Authors: Sikandar, A. / Franz, L. / Adam, S. / Santos-Aberturas, J. / Horbal, L. / Luzhetskyy, A. / Truman, A.W. / Kalinina, O.V. / Koehnke, J.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionOct 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BotH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8892
Polymers33,0901
Non-polymers7991
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.655, 80.285, 89.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-516-

HOH

31A-563-

HOH

41A-613-

HOH

51A-616-

HOH

61A-636-

HOH

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Components

#1: Protein BotH


Mass: 33089.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. BC16019 (bacteria) / Gene: botH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: K4MHV9
#2: Chemical ChemComp-MQW / (4~{R})-2-[(1~{R})-1-[[(2~{S})-2-[[(2~{S})-3-methyl-2-[[(4~{Z},6~{S},9~{S},12~{S})-2,8,11-tris(oxidanylidene)-6,9-di(propan-2-yl)-1,4,7,10-tetrazabicyclo[10.3.0]pentadec-4-en-5-yl]amino]butanoyl]amino]-3-phenyl-propanoyl]amino]-3-oxidanyl-3-oxidanylidene-propyl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid


Mass: 798.949 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H54N8O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 35.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: MES, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.25→44.77 Å / Num. obs: 65761 / % possible obs: 99.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 9.71 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.4
Reflection shellResolution: 1.25→1.27 Å / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 3355

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T6H

6t6h


Resolution: 1.25→44.77 Å / SU ML: 0.1007 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.264 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1752 3282 4.99 %
Rwork0.1661 62479 -
obs0.1666 65761 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.29 Å2
Refinement stepCycle: LAST / Resolution: 1.25→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 56 306 2291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842036
X-RAY DIFFRACTIONf_angle_d1.22862763
X-RAY DIFFRACTIONf_chiral_restr0.0808293
X-RAY DIFFRACTIONf_plane_restr0.008374
X-RAY DIFFRACTIONf_dihedral_angle_d15.2299726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.25851410.21152705X-RAY DIFFRACTION99.96
1.27-1.290.21011420.21142682X-RAY DIFFRACTION99.96
1.29-1.310.18621540.20092724X-RAY DIFFRACTION99.9
1.31-1.330.20461210.20312720X-RAY DIFFRACTION99.86
1.33-1.360.22591340.20362725X-RAY DIFFRACTION99.79
1.36-1.380.22881410.1992696X-RAY DIFFRACTION99.61
1.38-1.410.21871470.18952739X-RAY DIFFRACTION99.93
1.41-1.440.21081280.192703X-RAY DIFFRACTION99.09
1.44-1.470.21251490.17992697X-RAY DIFFRACTION99.86
1.47-1.510.17091510.17322731X-RAY DIFFRACTION99.97
1.51-1.550.18561540.1712720X-RAY DIFFRACTION99.9
1.55-1.60.20581250.16782765X-RAY DIFFRACTION99.86
1.6-1.650.18281160.16732700X-RAY DIFFRACTION99.65
1.65-1.710.18971520.16882731X-RAY DIFFRACTION99.38
1.71-1.780.17961440.16782659X-RAY DIFFRACTION97.87
1.78-1.860.16061490.15732747X-RAY DIFFRACTION99.69
1.86-1.960.16471470.15492723X-RAY DIFFRACTION99.34
1.96-2.080.15481380.14362755X-RAY DIFFRACTION99.38
2.08-2.240.16151370.14542707X-RAY DIFFRACTION98.65
2.24-2.460.1341510.14622693X-RAY DIFFRACTION97.43
2.46-2.820.16811710.15762657X-RAY DIFFRACTION96.95
2.82-3.550.14751450.16162730X-RAY DIFFRACTION97.26
3.55-44.770.18891450.16912770X-RAY DIFFRACTION94.37
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8390733361980.136081276392-0.04814431226041.8811084084-0.04590423513421.08366978284-0.005019508354240.0832965482851-0.0587384510331-0.0821143439040.0288445296495-0.1159632215160.07320829766430.0399635165202-0.01463641942120.0392772733393-0.001007254278630.002032476958970.0616611199464-0.001221699904760.0402474763683-6.58728644497-11.3870995236-34.6068398406
21.63223790838-0.0856192955150.05236794326321.798402756121.022429790572.62279780516-0.01613515671490.05012185970090.0946471983098-0.0841823619791-0.04387694183750.04084013848850.0335915855263-0.08357553386760.03906611037920.0507017034958-0.0107418506570.001683798677110.03188720797490.03327476954440.0326714089138-12.8437002475-1.72766403846-35.0092370605
31.507471552860.267786835282-0.09963100607221.69312625347-0.04941549503830.933571732167-0.01562091070090.01283773941080.0889673282810.0597092894107-0.003017491858970.12901753879-0.0214993264309-0.05835320431190.01829188570520.032403085186-0.0144107425966-0.0005602470392120.04799203819840.0106553411780.0570456909768-21.5444899436-10.7368249896-30.2327151597
41.40406960078-0.9717856834010.5257934522983.7692178512-0.7502320431471.4583982467-0.0705231677907-0.2472580195020.1059730197230.3335885400270.02178131409760.0418463649126-0.0322031153724-0.1154446501880.03922974372070.1303001348280.008311618817710.01497271788980.130360468371-0.01225440531030.0774403930758-11.7045396706-0.328899461687-11.670043413
50.936677933021.320080216560.2531113225413.79114092225-1.182658201321.331973910310.0604356241157-0.0894322786182-0.03213428672480.25677596648-0.05240513530930.0210965243053-0.0240180960002-0.0102710334489-0.02747362839470.08864002567860.004593570404360.002150354152910.0870881255458-0.001726418314320.0863718585979-5.18983347064-9.03761991627-17.2529181489
60.8810514480020.4875602183950.1907849585081.331881094060.2344472014870.29692842023-0.04635919918780.0194808978830.090535688866-0.005034669234240.01702766156130.202940183668-0.00713920007084-0.06738254537870.04300463281480.0583869412856-0.005582567263180.01364555879940.08974950578620.003107395902970.0716190913538-23.1717064395-8.45062751614-25.9976767455
71.87044926025-0.144564492034-0.3238233406530.8278229129340.03782048465051.02952921356-0.0295215281707-0.0499058151831-0.05981150891820.06816612155070.03001789699590.07911111114470.120391667139-0.04776401755440.006114035860310.080564032112-0.02183068790940.01055428035870.04770166842410.01150081286690.0506053919761-20.8031959554-21.4893435532-24.0327931814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 141 )
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 167 )
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 182 )
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 221 )
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 262 )

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