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- PDB-6wtf: Structure of radical S-adenosylmethionine methyltransferase, TsrM... -

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Basic information

Entry
Database: PDB / ID: 6wtf
TitleStructure of radical S-adenosylmethionine methyltransferase, TsrM, from Kitasatospora setae with tryptophan substrate and SAM analog (aza-SAM) bound
ComponentsTryptophan-C2-methyltransferase containing B12-binding domain
KeywordsTRANSFERASE / Radical SAM / Cobalamin / FeS cluster / methyltransferase
Function / homology
Function and homology information


cobalamin binding / catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
Tryptophan 2-C-methyltransferase / : / Radical SAM, alpha/beta horseshoe / B12 binding domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM
Similarity search - Domain/homology
COBALAMIN / S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / IRON/SULFUR CLUSTER / TRYPTOPHAN / Uncharacterized protein
Similarity search - Component
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKnox, H.L. / Chen, P.Y.-T. / Drennan, C.L. / Booker, S.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-12259 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-126982 United States
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Structural basis for non-radical catalysis by TsrM, a radical SAM methylase.
Authors: Knox, H.L. / Chen, P.Y. / Blaszczyk, A.J. / Mukherjee, A. / Grove, T.L. / Schwalm, E.L. / Wang, B. / Drennan, C.L. / Booker, S.J.
History
DepositionMay 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 7, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Tryptophan-C2-methyltransferase containing B12-binding domain
B: Tryptophan-C2-methyltransferase containing B12-binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,80910
Polymers128,2732
Non-polymers4,5358
Water6,792377
1
A: Tryptophan-C2-methyltransferase containing B12-binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4045
Polymers64,1371
Non-polymers2,2684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-36 kcal/mol
Surface area19720 Å2
MethodPISA
2
B: Tryptophan-C2-methyltransferase containing B12-binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4045
Polymers64,1371
Non-polymers2,2684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-36 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.355, 103.085, 105.757
Angle α, β, γ (deg.)90.000, 94.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 165 or resid 180...
21(chain B and (resid 2 through 360 or resid 362...

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
11SERSERPROPRO(chain A and (resid 2 through 165 or resid 180...AA2 - 1652 - 165
12PROPROTHRTHR(chain A and (resid 2 through 165 or resid 180...AA180 - 360180 - 360
13ARGARGPROPRO(chain A and (resid 2 through 165 or resid 180...AA362 - 517362 - 517
14HISHISGLUGLU(chain A and (resid 2 through 165 or resid 180...AA525 - 563525 - 563
21SERSERTHRTHR(chain B and (resid 2 through 360 or resid 362...BB2 - 3602 - 360
22ARGARGPROPRO(chain B and (resid 2 through 360 or resid 362...BB362 - 483362 - 483
23TRPTRPPROPRO(chain B and (resid 2 through 360 or resid 362...BB495 - 517495 - 517
24HISHISGLUGLU(chain B and (resid 2 through 360 or resid 362...BB525 - 563525 - 563

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tryptophan-C2-methyltransferase containing B12-binding domain


Mass: 64136.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora setae (bacteria)
Strain: ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054
Gene: KSE_17820 / Production host: Escherichia coli (E. coli) / References: UniProt: E4N8S5

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Non-polymers , 5 types, 385 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SA8 / S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / 5'-[N-[(3S)-3-AMINO-3-CARBOXYPROPYL]-N-METHYLAMINO]-5'-DEOXYADENOSINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M tri-sodium citrate, pH 5.6, 20% (v/v) isopropanol, 20% (w/v) PEG 4000, and 0.05 M nickel (II) dichloride hexahydrate

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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: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 53942 / % possible obs: 97.1 % / Redundancy: 4.8 % / CC1/2: 0.8 / Net I/σ(I): 6.47
Reflection shellResolution: 2.19→2.27 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 4655 / CC1/2: 0.8 / Rpim(I) all: 0.28

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WTE

6wte


Resolution: 2.19→46.92 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 2689 4.98 %
Rwork0.211 51253 -
obs0.2129 53942 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.36 Å2 / Biso mean: 23.4202 Å2 / Biso min: 12.61 Å2
Refinement stepCycle: final / Resolution: 2.19→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8503 0 282 377 9162
Biso mean--18.35 23.18 -
Num. residues----1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049037
X-RAY DIFFRACTIONf_angle_d0.67212331
X-RAY DIFFRACTIONf_dihedral_angle_d22.0483440
X-RAY DIFFRACTIONf_chiral_restr0.0451323
X-RAY DIFFRACTIONf_plane_restr0.0041679
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5095X-RAY DIFFRACTION4.633TORSIONAL
12B5095X-RAY DIFFRACTION4.633TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.230.35431370.28982567270494
2.23-2.270.38441360.33182731286798
2.27-2.320.31561410.26772694283598
2.32-2.370.3081450.24762747289298
2.37-2.420.28691470.2342698284598
2.42-2.480.29351460.24262693283998
2.48-2.550.30911350.23742716285197
2.55-2.620.30381460.22912716286298
2.62-2.710.23621360.22732652278896
2.71-2.810.27511440.2292738288298
2.81-2.920.29281430.24122682282598
2.92-3.050.29491450.2262723286898
3.05-3.210.24761380.22372717285598
3.21-3.410.24231390.21492694283396
3.41-3.680.2421450.19482697284297
3.68-4.050.21251420.17072682282497
4.05-4.630.17521440.14982716286097
4.63-5.830.15951410.16132684282596
5.83-46.920.21111390.18822706284595

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