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

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Basic information

Entry
Database: PDB / ID: 7kdy
TitleCrystal structure of Streptomyces tokunonesis TokK with hydroxycobalamin, 5'-deoxyadenosine, methionine, and (2R)-pantetheinylated carbapenam
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 / Chem-WCD / Methyltransferase TokK
Similarity search - Component
Biological speciesStreptomyces tokunonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.939 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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)159,85417
Polymers154,9172
Non-polymers4,93715
Water21,4921193
1
A: Methyltransferase TokK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1439
Polymers77,4591
Non-polymers2,6848
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase TokK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7118
Polymers77,4591
Non-polymers2,2537
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.503, 132.817, 155.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 168 or resid 170...
21(chain B and (resid 9 through 168 or resid 170...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPRO(chain A and (resid 9 through 168 or resid 170...AA9 - 1689 - 168
12LEULEUTYRTYR(chain A and (resid 9 through 168 or resid 170...AA170 - 208170 - 208
13CYSCYSCYSCYS(chain A and (resid 9 through 168 or resid 170...AA210210
14THRTHRPHEPHE(chain A and (resid 9 through 168 or resid 170...AA222 - 424222 - 424
15METMETGLYGLY(chain A and (resid 9 through 168 or resid 170...AA426 - 454426 - 454
16TYRTYRMETMET(chain A and (resid 9 through 168 or resid 170...AA456 - 498456 - 498
17SERSERLEULEU(chain A and (resid 9 through 168 or resid 170...AA500 - 672500 - 672
18HOHHOHHOHHOH(chain A and (resid 9 through 168 or resid 170...AR901
21GLYGLYPROPRO(chain B and (resid 9 through 168 or resid 170...BB9 - 1689 - 168
22LEULEUTYRTYR(chain B and (resid 9 through 168 or resid 170...BB170 - 208170 - 208
23CYSCYSMETMET(chain B and (resid 9 through 168 or resid 170...BB210 - 220210 - 220
24THRTHRPHEPHE(chain B and (resid 9 through 168 or resid 170...BB222 - 424222 - 424
25METMETGLYGLY(chain B and (resid 9 through 168 or resid 170...BB426 - 454426 - 454
26TYRTYRMETMET(chain B and (resid 9 through 168 or resid 170...BB456 - 498456 - 498
27SERSERASPASP(chain B and (resid 9 through 168 or resid 170...BB500 - 567500 - 567
28ALAALALEULEU(chain B and (resid 9 through 168 or resid 170...BB572 - 672572 - 672
29HOHHOHHOHHOH(chain B and (resid 9 through 168 or resid 170...BS901

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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, 1208 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-B12 / COBALAMIN / Vitamin B12


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


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-WCD / (2R,3R,5R)-3-{[2-({N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid / (2R)-pantetheinylated carbapenam


Mass: 431.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H29N3O7S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1193 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, and 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.939→50 Å / Num. obs: 129910 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.998 / Net I/σ(I): 58.5
Reflection shellResolution: 1.94→1.97 Å / Num. unique obs: 6430 / CC1/2: 0.975

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1000252295

Resolution: 1.939→44.185 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1875 3010 1.54 %
Rwork0.1568 192225 -
obs0.1572 129910 77.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.03 Å2 / Biso mean: 24.9169 Å2 / Biso min: 2.14 Å2
Refinement stepCycle: final / Resolution: 1.939→44.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10635 0 297 1193 12125
Biso mean--17.28 31.77 -
Num. residues----1325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411276
X-RAY DIFFRACTIONf_angle_d0.75315372
X-RAY DIFFRACTIONf_chiral_restr0.0471610
X-RAY DIFFRACTIONf_plane_restr0.0052083
X-RAY DIFFRACTIONf_dihedral_angle_d12.9846799
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6320X-RAY DIFFRACTION4.572TORSIONAL
12B6320X-RAY DIFFRACTION4.572TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9395-1.97130.2308930.2143599251
1.9713-2.00520.223950.2009604752
2.0052-2.04170.2078950.197605352
2.0417-2.0810.2206950.1927614352
2.081-2.12350.2128970.1861623353
2.1235-2.16960.23521000.1826642055
2.1696-2.22010.23811100.1815659856
2.2201-2.27560.21951110.1711707960
2.2756-2.33710.17681250.1644783867
2.3371-2.40590.21321370.1575870574
2.4059-2.48360.20861560.156966782
2.4836-2.57230.17311640.16491045889
2.5723-2.67530.19361740.1711128796
2.6753-2.7970.18591830.16651164099
2.797-2.94450.19561790.16491167099
2.9445-3.12890.23191820.16611777100
3.1289-3.37040.17771890.160211691100
3.3704-3.70940.18961820.151211736100
3.7094-4.24580.16491790.130511743100
4.2458-5.34780.15281870.126711740100
5.3478-44.1850.16291770.150511708100
Refinement TLS params.Method: refined / Origin x: 3.0467 Å / Origin y: -9.4023 Å / Origin z: -32.9209 Å
111213212223313233
T-0.0795 Å2-0.0778 Å2-0.0691 Å2--0.007 Å2-0.0234 Å2---0.0158 Å2
L0.0667 °2-0.0118 °2-0.0289 °2-0.2218 °2-0.015 °2--0.0198 °2
S0.0345 Å °0.0679 Å °0.0497 Å °0.1324 Å °-0.0227 Å °-0.0366 Å °0.0035 Å °0.022 Å °0.047 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 672
2X-RAY DIFFRACTION1allA701 - 1401
3X-RAY DIFFRACTION1allB9 - 672
4X-RAY DIFFRACTION1allB701 - 1101
5X-RAY DIFFRACTION1allS12 - 1365
6X-RAY DIFFRACTION1allC1 - 4

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