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

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Basic information

Entry
Database: PDB / ID: 6wte
TitleStructure of radical S-adenosylmethionine methyltransferase, TsrM, from Kitasatospora setae with cobalamin and [4Fe-4S] cluster bound
ComponentsB12-binding domain-containing protein
KeywordsTRANSFERASE / Radical SAM / Cobalamin / FeS cluster / methyltransferase
Function / homology
Function and homology information


cobalamin binding / iron-sulfur cluster binding / catalytic activity / metal ion binding
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 / IRON/SULFUR CLUSTER / Tryptophanase
Similarity search - Component
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 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 1.3Mar 6, 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: B12-binding domain-containing protein
B: B12-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,75524
Polymers128,2732
Non-polymers4,48122
Water12,935718
1
A: B12-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,50114
Polymers64,1371
Non-polymers2,36513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: B12-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,25310
Polymers64,1371
Non-polymers2,1169
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.368, 103.759, 105.970
Angle α, β, γ (deg.)90.000, 95.080, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 79 or resid 81...
21(chain B and (resid 1 through 79 or resid 81...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 79 or resid 81...A1 - 79
121(chain A and (resid 1 through 79 or resid 81...A81 - 86
131(chain A and (resid 1 through 79 or resid 81...A145
141(chain A and (resid 1 through 79 or resid 81...A14165
151(chain A and (resid 1 through 79 or resid 81...A177 - 213
161(chain A and (resid 1 through 79 or resid 81...A21513
171(chain A and (resid 1 through 79 or resid 81...A225 - 337
181(chain A and (resid 1 through 79 or resid 81...A339 - 360
191(chain A and (resid 1 through 79 or resid 81...A363 - 367
1101(chain A and (resid 1 through 79 or resid 81...A369 - 40
1111(chain A and (resid 1 through 79 or resid 81...A409 - 430
1121(chain A and (resid 1 through 79 or resid 81...A432 - 463
1131(chain A and (resid 1 through 79 or resid 81...A465 - 482
1141(chain A and (resid 1 through 79 or resid 81...A495 - 519
1151(chain A and (resid 1 through 79 or resid 81...A532 - 546
1161(chain A and (resid 1 through 79 or resid 81...A548 - 565
1171(chain A and (resid 1 through 79 or resid 81...A801 - 802
211(chain B and (resid 1 through 79 or resid 81...B1 - 79
221(chain B and (resid 1 through 79 or resid 81...B81 - 86
231(chain B and (resid 1 through 79 or resid 81...B88 - 141
241(chain B and (resid 1 through 79 or resid 81...B143
251(chain B and (resid 1 through 79 or resid 81...B1 - 802
261(chain B and (resid 1 through 79 or resid 81...B215 - 223
271(chain B and (resid 1 through 79 or resid 81...B1 - 802
281(chain B and (resid 1 through 79 or resid 81...B339 - 360
291(chain B and (resid 1 through 79 or resid 81...B409 - 437
2101(chain B and (resid 1 through 79 or resid 81...B432 - 460
2111(chain B and (resid 1 through 79 or resid 81...B548 - 563
2121(chain B and (resid 1 through 79 or resid 81...B465 - 546
2131(chain B and (resid 1 through 79 or resid 81...B548 - 565
2141(chain B and (resid 1 through 79 or resid 81...B801 - 802

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Components

#1: Protein B12-binding domain-containing protein


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
#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: isolated from a natural source / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 718 / 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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium acetate, 0.1 M MES, pH 6.5, and 15% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 123027 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 10.72 Å2 / CC1/2: 0.8 / Net I/σ(I): 9.44
Reflection shellResolution: 1.66→1.73 Å / Mean I/σ(I) obs: 2.19 / Num. unique obs: 12117 / Rpim(I) all: 0.34 / Rsym value: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
AutoSolphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.67→43.14 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 6146 5 %
Rwork0.1898 116757 -
obs0.1911 122903 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.61 Å2 / Biso mean: 20.0901 Å2 / Biso min: 9.06 Å2
Refinement stepCycle: final / Resolution: 1.67→43.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8613 0 270 718 9601
Biso mean--17.83 24.78 -
Num. residues----1097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049331
X-RAY DIFFRACTIONf_angle_d0.73212714
X-RAY DIFFRACTIONf_dihedral_angle_d22.9993615
X-RAY DIFFRACTIONf_chiral_restr0.0491358
X-RAY DIFFRACTIONf_plane_restr0.0051711
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5024X-RAY DIFFRACTION4.828TORSIONAL
12B5024X-RAY DIFFRACTION4.828TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.67-1.690.30122090.29653869407899
1.69-1.710.33382040.280539144118100
1.71-1.730.30141960.269838204016100
1.73-1.750.28572100.258838664076100
1.75-1.770.29241970.243539084105100
1.77-1.80.22282040.229838544058100
1.8-1.820.26792100.22639604170100
1.82-1.850.23932070.21438224029100
1.85-1.880.25712020.20338754077100
1.88-1.910.23952040.203939064110100
1.91-1.940.24791990.192538724071100
1.94-1.980.22982100.189939154125100
1.98-2.020.23922110.189238264037100
2.02-2.060.22891950.18839324127100
2.06-2.10.23992080.18938264034100
2.1-2.150.23022020.184139354137100
2.15-2.210.20842060.177838764082100
2.21-2.270.20731990.180338744073100
2.27-2.330.21422110.177638824093100
2.33-2.410.20492040.178838824086100
2.41-2.490.20912050.183138924097100
2.49-2.590.19762070.181939444151100
2.59-2.710.19832030.183238584061100
2.71-2.860.22272040.194439174121100
2.86-3.030.21732050.196338924097100
3.03-3.270.20572090.191739244133100
3.27-3.60.20112040.179138974101100
3.6-4.120.19142050.166239344139100
4.12-5.190.1622070.160739124119100
5.19-43.140.18322090.181839734182100
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)
10.1527-0.0806-0.00760.70220.03520.42940.00440.0159-0.0047-0.0251-0.00070.0483-0.0088-0.0364-0.00420.1172-0.0031-0.0070.1182-0.00160.109547.62776.83665.2609
20.1997-0.0319-0.07580.7339-0.24610.6525-0.01560.02010.00570.0080.0138-0.044-0.00280.0064-0.00060.1588-0.0020.00540.11980.00010.109843.70675.388111.2381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A1 - 802
2X-RAY DIFFRACTION2chain 'B'B1 - 802

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