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- PDB-6t6y: Structure of the Bottromycin epimerase BotH in complex with Bottr... -

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Basic information

Entry
Database: PDB / ID: 6t6y
TitleStructure of the Bottromycin epimerase BotH in complex with Bottromycin A2
ComponentsBotH
KeywordsHYDROLASE / Bottromycin / RiPP / Epimerase / ABH
Function / homology: / alpha/beta hydrolase fold / catalytic activity / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / metal ion binding / Bottromycin A2 / BotH
Function and homology information
Biological speciesStreptomyces sp. BC16019 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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)33,9132
Polymers33,0901
Non-polymers8231
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.986, 80.109, 89.420
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-402-

HOH

21A-435-

HOH

31A-449-

HOH

41A-517-

HOH

51A-580-

HOH

61A-593-

HOH

71A-594-

HOH

81A-596-

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-MQH / Bottromycin A2


Mass: 823.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H62N8O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 1.81 Å3/Da / Density % sol: 32.14 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.4→44.71 Å / Num. obs: 47303 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2324 / % possible all: 99.5

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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: 1.4→44.71 Å / SU ML: 0.1171 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5335
RfactorNum. reflection% reflection
Rfree0.1823 2373 5.02 %
Rwork0.1592 --
obs0.1604 47297 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.14 Å2
Refinement stepCycle: LAST / Resolution: 1.4→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 58 225 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01632045
X-RAY DIFFRACTIONf_angle_d1.42552780
X-RAY DIFFRACTIONf_chiral_restr0.1057295
X-RAY DIFFRACTIONf_plane_restr0.0125375
X-RAY DIFFRACTIONf_dihedral_angle_d15.6687726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.26251310.22822633X-RAY DIFFRACTION99.35
1.43-1.460.231220.22012605X-RAY DIFFRACTION99.27
1.46-1.490.25211400.2052617X-RAY DIFFRACTION99.14
1.49-1.530.22621360.19592599X-RAY DIFFRACTION99.2
1.53-1.570.20341270.192619X-RAY DIFFRACTION99.35
1.57-1.620.19531450.16822614X-RAY DIFFRACTION99.64
1.62-1.670.18831310.16862651X-RAY DIFFRACTION99.53
1.67-1.730.19321450.16332606X-RAY DIFFRACTION99.35
1.73-1.80.15891560.1632636X-RAY DIFFRACTION99.36
1.8-1.880.17921440.15472605X-RAY DIFFRACTION99.35
1.88-1.980.1761370.14612646X-RAY DIFFRACTION99.04
1.98-2.110.1881250.13952668X-RAY DIFFRACTION99.82
2.11-2.270.15831580.14072628X-RAY DIFFRACTION99.54
2.27-2.50.17451410.14282659X-RAY DIFFRACTION98.9
2.5-2.860.16311420.14682646X-RAY DIFFRACTION98.41
2.86-3.60.17881470.1512708X-RAY DIFFRACTION99.76
3.6-44.710.18861460.17152784X-RAY DIFFRACTION98.62
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)
11.844967254670.688112815673-0.007805787396555.422725035060.4235125808142.24784308372-0.0243425357182-0.117907649623-0.04395985360820.0816309876021-0.0423338546060.190258216386-0.0099012760518-0.0828091500442-0.002469790371560.1284929227530.01729078642690.01360066833790.131403559249-0.01222996025030.115944020569-27.9377990177-3.92223241928-6.22445024301
22.164353256010.0555894551354-0.6260326497393.42538706107-0.8613724496093.695919164590.0079472797717-0.085629610147-0.1821348169060.04023405693090.01376807788010.1626909010720.108521256306-0.0834985902298-0.003427653865970.09711655354440.0209510835176-0.001084732811470.101148779495-0.02206168175850.119143139518-25.9788428709-13.2278501918-13.5947424242
31.71854992782-1.12390293408-0.4714594929183.24899418142-0.07740359545385.064207031550.05343237494030.0387621430138-0.2721214205960.1625606266060.1062487020820.07953385205260.548340867108-0.4884526883170.02558335138880.150837434131-0.0432323175084-0.01997720017140.1351350355450.002526119923880.177148701762-26.875777582-19.2874469119-10.6162567223
46.258354529951.84434794181-2.781012972524.47157365774-2.846155184685.4416960357-0.08607378837410.1579192022480.24839497445-0.1084038486560.08666693950620.00846303063129-0.0588982050651-0.0791424793805-0.03333453601240.1224082278670.0183915304062-0.003785240609130.106044273733-0.0211643349710.116628142679-23.73436166332.59729588515-15.7859966144
53.851710569510.250292418785-1.028626063893.03293759289-1.727304197455.93762897535-0.00675584560089-0.2391948235310.017708385810.207544170217-0.128761509035-0.07744154799270.09823125147740.2248042237820.0959871761210.1495158446460.0263928846461-0.0142515696890.127591248685-0.03471587394090.123856197573-18.5032065287-5.32359560528-4.94945336065
61.46913883302-0.5393609782910.2438411308051.34065908696-0.3708543698950.8326940068620.03535996863960.1990634243150.0646869303352-0.182568189683-0.0681030241763-0.1368906124090.0149999719670.08107700394510.0501901939780.1469516858940.0190456648310.02241391874830.147031853561-0.01415885863670.145314673932-15.8611967052-6.58469441996-21.9075855858
73.691321216-1.72920806580.4070544079697.063587071421.945501142074.201049292750.03394372970480.243080207718-0.186331735733-0.292717208936-0.003530443317610.1886835651740.0970774239191-0.04793226190560.04798786524190.1357545100150.00507250278224-0.006231825878970.173742062414-0.02838308590540.141306475339-28.1011167-9.51401444254-27.6512287521
82.72248352825-1.851246804581.210659682473.07012129178-1.197551677621.79502932368-0.0817295525478-0.08334379418860.2478642510990.01094602293950.0268916013173-0.384686142610.011918460210.06559858556260.03233428398460.1536143546770.008926873180630.01367810315330.176250208056-0.01849908374910.187767145166-10.6261644466-3.65743899873-16.3110840843
93.033094060290.2825661890330.4340872385562.018255920820.4629023384691.8086328364-0.06952640789270.160421082209-0.0739672106552-0.07064069545640.112913887642-0.1683190321150.08973632893750.171682051593-0.05461651540310.1603112552320.03146606153730.02781499111540.152692088378-0.02454289758440.177540895797-7.61611205437-19.7282163042-22.047268597
104.036351536870.961548129759-1.709869346065.23242273111-3.330976810152.6556988601-0.05240141182070.0416527809527-0.22410256094-0.165086241064-0.01048670466220.01537291418240.1829602012170.06265283860290.08148043166640.1843220755810.01605072788580.009405656477260.115566127753-0.04630973505070.159546046379-19.6173978997-23.2955357747-19.8960380762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 83 )
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 102 )
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 167 )
7X-RAY DIFFRACTION7chain 'A' and (resid 168 through 182 )
8X-RAY DIFFRACTION8chain 'A' and (resid 183 through 208 )
9X-RAY DIFFRACTION9chain 'A' and (resid 209 through 242 )
10X-RAY DIFFRACTION10chain 'A' and (resid 243 through 262 )

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