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- PDB-8gdu: Crystal structure of a mutant methyl transferase from Methanosarc... -

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Basic information

Entry
Database: PDB / ID: 8gdu
TitleCrystal structure of a mutant methyl transferase from Methanosarcina acetivorans, Northeast Structural Genomics Consortium (NESG) Target MvR53-11M
ComponentsMethyltransferase domain-containing protein
KeywordsTRANSFERASE / SAM-binding protein
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methyltransferase activity / methylation / metal ion binding
Similarity search - Function
TPMT family / Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile. / Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans C2A (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsForouhar, F. / Banayan, N.E. / Loughlin, B.L. / Singh, S. / Wong, V. / Hunt, H.S. / Handelman, S.K. / Price, N. / Hunt, J.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution.
Authors: Banayan, N.E. / Loughlin, B.J. / Singh, S. / Forouhar, F. / Lu, G. / Wong, K.H. / Neky, M. / Hunt, H.S. / Bateman Jr., L.B. / Tamez, A. / Handelman, S.K. / Price, W.N. / Hunt, J.F.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7562
Polymers23,3711
Non-polymers3841
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, crystal structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.950, 109.950, 39.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-433-

HOH

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Components

#1: Protein Methyltransferase domain-containing protein


Mass: 23371.484 Da / Num. of mol.: 1
Mutation: K8R, K52R, K64R, D65R, K71R, K126R, K129R, K133R, K142R, K155R, K172R, K194R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans C2A (archaea)
Gene: MA_2137 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TNZ0
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 7.5 / Details: 0.1 M HEPES and 30% (w/v) PEG 1k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.91→109.95 Å / Num. obs: 19350 / % possible obs: 99.8 % / Redundancy: 25.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Net I/σ(I): 20.4
Reflection shellResolution: 1.91→1.95 Å / Rmerge(I) obs: 2.828 / Num. unique obs: 1253 / CC1/2: 0.491 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→77.75 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 1642 9.93 %
Rwork0.1822 --
obs0.185 16541 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→77.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 26 89 1600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071544
X-RAY DIFFRACTIONf_angle_d1.0352087
X-RAY DIFFRACTIONf_dihedral_angle_d34.247580
X-RAY DIFFRACTIONf_chiral_restr0.067227
X-RAY DIFFRACTIONf_plane_restr0.006272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.070.24361340.22151219X-RAY DIFFRACTION100
2.07-2.140.25691310.19321200X-RAY DIFFRACTION100
2.14-2.210.2231320.18681226X-RAY DIFFRACTION100
2.21-2.30.23311350.17671222X-RAY DIFFRACTION100
2.3-2.410.2061380.17461204X-RAY DIFFRACTION100
2.41-2.530.20791350.18151220X-RAY DIFFRACTION100
2.53-2.690.23551340.17451233X-RAY DIFFRACTION100
2.69-2.90.19731310.171248X-RAY DIFFRACTION100
2.9-3.190.21651600.17451210X-RAY DIFFRACTION100
3.19-3.650.20261450.17431257X-RAY DIFFRACTION100
3.65-4.60.18741210.17561292X-RAY DIFFRACTION100
4.6-77.750.21491460.19861368X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -9.2734 Å / Origin y: 33.6148 Å / Origin z: 0.4888 Å
111213212223313233
T0.2714 Å2-0.0229 Å2-0.0046 Å2-0.2718 Å20.0145 Å2--0.2534 Å2
L1.8291 °21.0592 °2-0.3136 °2-1.7145 °20.3423 °2--1.8186 °2
S-0.0492 Å °-0.0266 Å °-0.1062 Å °0.0575 Å °-0.0342 Å °-0.0639 Å °0.2016 Å °-0.1559 Å °-0.0013 Å °
Refinement TLS groupSelection details: all

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