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- PDB-7kdx: Crystal structure of Streptomyces tokunonesis TokK with hydroxyco... -

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Basic information

Entry
Database: PDB / ID: 7kdx
TitleCrystal structure of Streptomyces tokunonesis TokK with hydroxycobalamin, 5'-deoxyadenosine, and methionine
ComponentsMethyltransferase TokK
KeywordsTRANSFERASE / Radical SAM / Cobalamin / [4Fe-4S] cluster / FeS cluster / methyltransferase / B12 / beta-lactam antibiotic synthesis
Function / homology
Function and homology information


cobalamin binding / iron-sulfur cluster binding / methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Carbapenem intermediate methyltransferase ThnK-like / Radical SAM, alpha/beta horseshoe / B12 binding domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Radical SAM core domain profile. / Radical SAM
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / : / METHIONINE / IRON/SULFUR CLUSTER / Methyltransferase TokK
Similarity search - Component
Biological speciesStreptomyces tokunonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.791 Å
AuthorsKnox, H.L. / Booker, S.J. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-12259 United States
CitationJournal: Nature / Year: 2022
Title: Structure of a B 12 -dependent radical SAM enzyme in carbapenem biosynthesis.
Authors: Knox, H.L. / Sinner, E.K. / Townsend, C.A. / Boal, A.K. / Booker, S.J.
History
DepositionOct 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase TokK
B: Methyltransferase TokK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,53535
Polymers154,9172
Non-polymers5,61733
Water15,979887
1
A: Methyltransferase TokK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,01513
Polymers77,4591
Non-polymers2,55612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyltransferase TokK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,52022
Polymers77,4591
Non-polymers3,06121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.644, 137.739, 77.914
Angle α, β, γ (deg.)90.000, 90.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 44 or resid 46...
21(chain B and (resid 9 through 44 or resid 46...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 9 through 44 or resid 46...A9 - 44
121(chain A and (resid 9 through 44 or resid 46...A46 - 78
131(chain A and (resid 9 through 44 or resid 46...A80 - 112
141(chain A and (resid 9 through 44 or resid 46...A212 - 220
151(chain A and (resid 9 through 44 or resid 46...A9 - 672
161(chain A and (resid 9 through 44 or resid 46...A222 - 241
171(chain A and (resid 9 through 44 or resid 46...A9 - 672
181(chain A and (resid 9 through 44 or resid 46...A279 - 304
191(chain A and (resid 9 through 44 or resid 46...A9 - 672
1101(chain A and (resid 9 through 44 or resid 46...A357 - 408310
1111(chain A and (resid 9 through 44 or resid 46...A425 - 423
1121(chain A and (resid 9 through 44 or resid 46...A425 - 442
1131(chain A and (resid 9 through 44 or resid 46...A444 - 454
1141(chain A and (resid 9 through 44 or resid 46...A540 - 668
1151(chain A and (resid 9 through 44 or resid 46...A540 - 662
1161(chain A and (resid 9 through 44 or resid 46...A664 - 665
1171(chain A and (resid 9 through 44 or resid 46...A667 - 1101
211(chain B and (resid 9 through 44 or resid 46...B9 - 44
221(chain B and (resid 9 through 44 or resid 46...B46 - 78
231(chain B and (resid 9 through 44 or resid 46...B80 - 112
241(chain B and (resid 9 through 44 or resid 46...B114 - 140
251(chain B and (resid 9 through 44 or resid 46...B212 - 220
261(chain B and (resid 9 through 44 or resid 46...B7 - 672
271(chain B and (resid 9 through 44 or resid 46...B222 - 241
281(chain B and (resid 9 through 44 or resid 46...B243 - 276
291(chain B and (resid 9 through 44 or resid 46...B410 - 4
2101(chain B and (resid 9 through 44 or resid 46...B357 - 40
2111(chain B and (resid 9 through 44 or resid 46...B416 - 418
2121(chain B and (resid 9 through 44 or resid 46...B420 - 423
2131(chain B and (resid 9 through 44 or resid 46...B425 - 442
2141(chain B and (resid 9 through 44 or resid 46...B444 - 45499
2151(chain B and (resid 9 through 44 or resid 46...B50157
2161(chain B and (resid 9 through 44 or resid 46...B459 - 499
2171(chain B and (resid 9 through 44 or resid 46...B501 - 53665
2181(chain B and (resid 9 through 44 or resid 46...B664 - 665
2191(chain B and (resid 9 through 44 or resid 46...B667 - 10

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methyltransferase TokK


Mass: 77458.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tokunonensis (bacteria) / Gene: tokK / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B9HEI0

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Non-polymers , 8 types, 920 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM magnesium chloride, 100 mM calcium chloride, 20% PEG 8000, and 10% 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03313 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03313 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 132404 / % possible obs: 97.8 % / Redundancy: 6.7 % / CC1/2: 0.78 / Net I/σ(I): 4.9
Reflection shellResolution: 1.79→1.82 Å / Rmerge(I) obs: 0.84 / Num. unique obs: 6514

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
AutoSolphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.791→41.353 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 3738 2.01 %
Rwork0.1648 181930 -
obs0.1654 132404 69.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.33 Å2 / Biso mean: 26.0535 Å2 / Biso min: 6.48 Å2
Refinement stepCycle: final / Resolution: 1.791→41.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10607 0 340 887 11834
Biso mean--20.39 34.81 -
Num. residues----1322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511371
X-RAY DIFFRACTIONf_angle_d0.69915461
X-RAY DIFFRACTIONf_chiral_restr0.0461618
X-RAY DIFFRACTIONf_plane_restr0.0042093
X-RAY DIFFRACTIONf_dihedral_angle_d13.6856839
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6052X-RAY DIFFRACTION6.692TORSIONAL
12B6052X-RAY DIFFRACTION6.692TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7911-1.81370.2754750.2273393940
1.8137-1.83760.2009870.2242416343
1.8376-1.86280.2606880.2163442245
1.8628-1.88940.2231990.2222466648
1.8894-1.91760.2401930.2195473948
1.9176-1.94750.26271030.2149475549
1.9475-1.97950.24970.2177478649
1.9795-2.01360.2278970.2136483750
2.0136-2.05020.22721050.2053489850
2.0502-2.08970.2435990.1982496351
2.0897-2.13230.22671060.1858517653
2.1323-2.17870.20471000.1818537155
2.1787-2.22930.21681370.1771567658
2.2293-2.28510.18591210.1719600762
2.2851-2.34690.22361340.1751654667
2.3469-2.41590.18521500.1727700172
2.4159-2.49390.22941350.171752377
2.4939-2.5830.21291580.173803082
2.583-2.68640.23371750.1704865689
2.6864-2.80870.20111960.1708902793
2.8087-2.95670.22771930.1673950697
2.9567-3.14190.19662000.1646957198
3.1419-3.38440.18261960.1558958098
3.3844-3.72470.16152040.1499958398
3.7247-4.26330.1851940.1378960299
4.2633-5.36940.13811980.1402953498
5.3694-41.3530.17931980.1592937396
Refinement TLS params.Method: refined / Origin x: 1.5505 Å / Origin y: 5.5522 Å / Origin z: -30.5336 Å
111213212223313233
T-0.0013 Å2-0.011 Å20.0589 Å2-0.1103 Å2-0.0076 Å2--0.0358 Å2
L0.0442 °20.2925 °20.2416 °2-0.7024 °20.2799 °2--0.1168 °2
S0.0109 Å °-0.0095 Å °0.0064 Å °0.0476 Å °-0.0132 Å °-0.0138 Å °-0.0238 Å °-0.0114 Å °-0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 672
2X-RAY DIFFRACTION1allA701 - 2401
3X-RAY DIFFRACTION1allB7 - 672
4X-RAY DIFFRACTION1allB701 - 3001
5X-RAY DIFFRACTION1allS3 - 1424
6X-RAY DIFFRACTION1allC1 - 2
7X-RAY DIFFRACTION1allD2 - 3

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