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- PDB-2k4m: Solution NMR Structure of M. thermoautotrophicum protein MTH_1000... -

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Basic information

Entry
Database: PDB / ID: 2k4m
TitleSolution NMR Structure of M. thermoautotrophicum protein MTH_1000, Northeast Structural Genomics Consortium Target TR8
ComponentsUPF0146 protein MTH_1000
Keywordsstructural genomics / unknown function / alpha+beta / Rossmann fold / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyUncharacterised protein family UPF0146 / Uncharacterised protein family (UPF0146) / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / UPF0146 protein MTH_1000
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsEletsky, A. / Sukumaran, D. / Semesi, A. / Guido, V. / Yee, A. / Arrowsmith, C. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of M. thermoautotrophicum protein MTH_1000, Northeast Structural Genomics Consortium Target TR8
Authors: Eletsky, A. / Sukumaran, D. / Semesi, A. / Guido, V. / Yee, A. / Arrowsmith, C. / Szyperski, T.
History
DepositionJun 13, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0146 protein MTH_1000


Theoretical massNumber of molelcules
Total (without water)17,2841
Polymers17,2841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein UPF0146 protein MTH_1000 / TR8_protein


Mass: 17283.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Genus: Methanobacterium / Species: thermoautotrophicum / Gene: MTH_1000 / Plasmid: pET15b / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold magic / References: UniProt: O27081

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CB
1513D HNCA
1613D CBCA(CO)NH
1713D HBHA(CO)NH
1813D 1H-15N,13Cali,13Caro NOESY
1913D (H)CCH-COSY aliphatic
11013D (H)CCH-TOCSY aliphatic
11113D (H)CCH-COSY aromatic
21222D 1H-13C HSQC methyl
21322D LR 1H-15N HSQC (His)

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Sample preparation

Details
Solution-IDContents
10.8 mM [U-100% 13C; U-100% 15N] TR8 protein, 10 mM sodium phosphate, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 90% H2O/10% D2O
20.8 mM [U-5% 13C; U-100% 15N] TR8 protein, 10 mM sodium phosphate, 450 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMTR8 protein[U-100% 13C; U-100% 15N]1
10 mMsodium phosphate1
300 mMsodium chloride1
1 mMbenzamidine1
10 mMDTT1
0.8 mMTR8 protein[U-5% 13C; U-100% 15N]2
10 mMsodium phosphate2
450 mMsodium chloride2
1 mMbenzamidine2
10 mMDTT2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
13006.5ambient 298 K
24506.5ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
VNMR6.1CVariancollection
VnmrJ2.1BVariancollection
PROSA6.0.2Guntertprocessing
XEASY1.3.13Bartels et al.data analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CSI2Wishart and Sykesdata analysis
TALOS2003.027.13.05Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
AutoAssign1.15.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVSBhattacharya and Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1929 / NOE intraresidue total count: 611 / NOE long range total count: 578 / NOE medium range total count: 266 / NOE sequential total count: 474
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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