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- PDB-6t6h: Apo structure of the Bottromycin epimerase BotH -

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Basic information

Entry
Database: PDB / ID: 6t6h
TitleApo structure of the Bottromycin epimerase BotH
ComponentsBotH
KeywordsHYDROLASE / Bottromycin / RiPP / Epimerase / ABH
Function / homologyalpha/beta hydrolase fold / catalytic activity / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / metal ion binding / BotH
Function and homology information
Biological speciesStreptomyces sp. BC16019 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.18 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 18, 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)33,4976
Polymers33,0901
Non-polymers4075
Water5,711317
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)66.683, 80.133, 88.699
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-199-

ARG

21A-401-

HOH

31A-533-

HOH

41A-550-

HOH

51A-567-

HOH

61A-637-

HOH

71A-638-

HOH

81A-652-

HOH

91A-712-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
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: 1.85 Å3/Da / Density % sol: 33.68 %
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: SLS / Beamline: X06DA / Wavelength: 0.97794 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97794 Å / Relative weight: 1
ReflectionResolution: 1.17→51.26 Å / Num. obs: 77123 / % possible obs: 98.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.51 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 21.4
Reflection shellResolution: 1.17→1.2 Å / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5273 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data reduction
XDSdata scaling
AutoSolphasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.18→51.26 Å / SU ML: 0.101 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.6692 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.168 3770 4.89 %
Rwork0.1569 73353 -
obs0.1574 77123 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.86 Å2
Refinement stepCycle: LAST / Resolution: 1.18→51.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 21 317 2267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111987
X-RAY DIFFRACTIONf_angle_d1.13882694
X-RAY DIFFRACTIONf_chiral_restr0.0916285
X-RAY DIFFRACTIONf_plane_restr0.0103363
X-RAY DIFFRACTIONf_dihedral_angle_d14.2842714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.190.2504980.24881882X-RAY DIFFRACTION68.51
1.19-1.210.26221460.24072560X-RAY DIFFRACTION94.19
1.21-1.220.24461380.23362618X-RAY DIFFRACTION94.09
1.22-1.240.21381310.21542632X-RAY DIFFRACTION95.84
1.24-1.260.22291250.21472671X-RAY DIFFRACTION96.81
1.26-1.280.22481320.20082688X-RAY DIFFRACTION97.92
1.28-1.30.20631480.20152714X-RAY DIFFRACTION98.79
1.3-1.320.21581550.20052718X-RAY DIFFRACTION99.03
1.32-1.350.19991420.19452721X-RAY DIFFRACTION99.03
1.35-1.370.21591760.19142719X-RAY DIFFRACTION99.42
1.37-1.40.22611390.18612757X-RAY DIFFRACTION99.52
1.4-1.430.19131410.18182738X-RAY DIFFRACTION99.48
1.43-1.460.24261260.17452745X-RAY DIFFRACTION99.62
1.46-1.50.17771450.16882756X-RAY DIFFRACTION99.66
1.5-1.540.22281540.16452765X-RAY DIFFRACTION99.79
1.54-1.590.17341280.16272778X-RAY DIFFRACTION99.83
1.59-1.640.16011360.15482754X-RAY DIFFRACTION99.79
1.64-1.70.18641420.15122767X-RAY DIFFRACTION99.93
1.7-1.760.15561310.15362803X-RAY DIFFRACTION99.93
1.76-1.840.14951410.15072784X-RAY DIFFRACTION99.97
1.84-1.940.17461430.14532775X-RAY DIFFRACTION99.83
1.94-2.060.15751400.13842788X-RAY DIFFRACTION99.9
2.06-2.220.15051550.14072786X-RAY DIFFRACTION99.9
2.22-2.450.16421310.13262811X-RAY DIFFRACTION99.66
2.45-2.80.1551520.14312806X-RAY DIFFRACTION99.97
2.8-3.530.14121340.14822853X-RAY DIFFRACTION99.57
3.53-51.260.14791410.15512964X-RAY DIFFRACTION99.58
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)
12.697179819611.17123189162-0.07017829102822.536130882720.155273189131.54749275013-0.00806651936856-0.117010317987-0.04437804554120.073239063667-0.01066079680560.1565988192-0.0117348971356-0.01897700900140.03477707868890.09073442919270.01521217941370.01132887772270.0909763882404-0.009227224086950.0771575920856-27.7440611994-3.93355697904-6.25395727825
21.33227522776-0.0401911400075-0.08419944866723.47257441572-2.105599293424.29654710253-0.0204582978993-0.0954914835332-0.07803898488060.07119633608720.07664257917390.1271468705210.101662524315-0.110518445727-0.06309751773910.07400068850410.01272839214010.009800768341530.0927466227647-0.003998111653780.0871865334608-26.0130394858-15.7428239777-12.3032424064
31.536172798070.155915738382-0.03042019192582.64710884667-2.421827658444.33677790842-0.00849044965102-0.01844950585610.04007066323290.057762516855-0.0775910004387-0.04797151184230.02879565410310.1351890348510.0705440678950.09457667741870.01771848443080.004798295105440.0667887460298-0.03057148244740.073603342323-20.5187905222-1.63944767167-9.81051273983
41.43207224732-0.216892390856-0.6587331767631.5969088015-0.09908335877021.61759814865-0.0102752215363-0.05377805170510.0690163316701-0.04363199934580.00780044151354-0.144751992098-0.05606209232980.1195188228220.002291023600280.08493996802180.0153594311314-0.00902142969260.0968013949447-0.01070948762540.107665115145-11.6360913617-10.68080697-14.5533072047
52.305749226182.279268198211.868107529357.012757566192.22651541221.7288659339-0.1194691969220.4221548622870.0268155854111-0.3337305444760.116239982687-0.132451129369-0.06673239790370.2195558369750.0006986963000390.181784320448-0.01232847439230.02036467911730.2034834096150.01909654373740.0967680883993-21.6872337633-0.386756250211-33.2763501602
64.59813204483-5.05581003819-1.687220997658.572161428795.887208408096.882396024590.03994392803520.118735064004-0.107452715697-0.249816309539-0.0288859997318-0.03254489991220.0640956840537-0.01186620097450.0571144369060.0867813106054-0.01949218455090.009124816753860.1033210838710.008224745080510.085768464922-27.9100628349-9.80670865527-27.6895215363
70.7748104435-0.536322469515-0.02893831722331.59957563666-0.1991899614180.0591471305684-0.0587152154314-0.06355991435930.0679494455650.01636963087170.0508437615882-0.219139830453-0.01745635424040.05707727445250.007877879908570.1112931060450.007012174464420.00249331071210.13633594711-0.007895555590430.118513738151-10.0489791857-8.51529256758-18.8353498994
82.953140268970.6787041794470.360622243451.14258657930.279248405232.0900371862-0.001401905676840.0264072388238-0.0561007374027-0.00619627668360.0501490206434-0.1615359823530.08596655336020.172653524455-0.05126559994480.1172156072720.02952467704080.01993965908090.102556163292-0.008574213521270.137053948406-6.32090419476-20.0752010224-21.438117775
92.746290857410.497671970561-1.539061800342.91894432869-2.788703878377.29610064183-0.15788640174-0.00554480099173-0.134389568449-0.07195454445630.0784826378584-0.01826014958670.184514537257-0.1467600575020.0747021479230.1442356424250.0181286812590.003079340182860.0783740669152-0.02828142917710.1044788299-19.2638658827-23.4093889511-19.580071076
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 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 141 )
5X-RAY DIFFRACTION5chain 'A' and (resid 142 through 167 )
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 182 )
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 221 )
8X-RAY DIFFRACTION8chain 'A' and (resid 222 through 242 )
9X-RAY DIFFRACTION9chain 'A' and (resid 243 through 262 )

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