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- PDB-1z9v: Solution Structure of MTH0776 from Methanobacterium thermoautotro... -

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Basic information

Entry
Database: PDB / ID: 1z9v
TitleSolution Structure of MTH0776 from Methanobacterium thermoautotrophicum (strain H)
Componentsconserved hypothetical protein MTH0776
KeywordsUNKNOWN FUNCTION / Solution Structure / Archaeabacterium
Function / homologyMTH0776-like / Domain of unknown function (DUF1894) / : / Conserved protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / simulated annealing protocol in XPLOR-NIH
AuthorsAmegbey, G. / Stothard, P. / Iakounine, A. / Yee, A. / Arrowsmith, C.H. / Wishart, D.S.
CitationJournal: J.Biomol.Nmr / Year: 2005
Title: Solution Structure of MTH0776 from Methanobacterium Thermoautotrophicum.
Authors: Amegbey, G. / Stothard, P. / Kuznetsova, E. / Yee, A. / Arrowsmith, C.H. / Wishart, D.S.
History
DepositionApr 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein MTH0776


Theoretical massNumber of molelcules
Total (without water)13,5841
Polymers13,5841
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 / 60structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein conserved hypothetical protein MTH0776


Mass: 13583.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: MTH776 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 2621867, UniProt: O26870*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB, HNCA, CBCA(CO)NH, HNCO, H(CCO)NH, C(CO)NH, 15N-separated NOESY
222D2O-exchange 15N HSQC, 13C-separated NOESY, (H)CCH-TOCSY
333HNHA
4442D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM MTH0776 U-15N,13C; 50mM NaH2PO4 buffer pH6.8, 300mM NaCl, 0.1mM DSS, 15mM DTT, 0.06% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
21mM MTH0776 U-15N,13C; 50mM NaH2PO4 buffer pH6.8, 300mM NaCl, 0.1mM DSS, 15mM DTT, 0.06% NaN3, 100% D2O100% D20
31mM MTH0776 U-15N; 50mM NaH2PO4 buffer pH6.8, 300mM NaCl, 0.1mM DSS, 15mM DTT, 0.06% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
41mM MTH0776 unlabelled; 50mM NaH2PO4 buffer pH6.8, 300mM NaCl, 0.1mM DSS, 15mM DTT, 0.06% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300mM NaCl, 50mM NaH2PO4 6.8ambient 298 K
2300mM NaCl, 50mM NaH2PO4 6.8ambient 298 K
3300mM NaCl, 50mM NaH2PO4 6.8ambient 298 K
4300mM NaCl, 50mM NaH2PO4 6.8ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Ccollection
NMRPipeDelaglio, F., Grzesiek, S., Vuister, G., Zhu, G., Pfeifer, J. and Bax, A.processing
XPLOR-NIH2.9.6refinement
RefinementMethod: simulated annealing protocol in XPLOR-NIH / Software ordinal: 1
Details: The structures are based on a total of 2048 restraints, 1844 are NOE-derived distance constraints, 164 dihedral angle restraints, 40 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 20

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