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- PDB-1pu1: Solution structure of the Hypothetical protein mth677 from Methan... -

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Basic information

Entry
Database: PDB / ID: 1pu1
TitleSolution structure of the Hypothetical protein mth677 from Methanothermobacter Thermautotrophicus
ComponentsHypothetical protein MTH677Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha and beta protein (a+b)
Function / homologyMTH677-like / Protein of unknown function DUF3194 / MTH677-like superfamily / Protein of unknown function (DUF3194) / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein MTH_677
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / distance geometry plus molecular mechanics
AuthorsBlanco, F.J. / Yee, A. / Campos-Olivas, R. / Devos, D. / Valencia, A. / Arrowsmith, C.H. / Rico, M.
CitationJournal: Protein Sci. / Year: 2004
Title: Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: A novel {alpha}+{beta} fold
Authors: Blanco, F.J. / Yee, A. / Campos-Olivas, R. / Ortiz, A.R. / Devos, D. / Valencia, A. / Arrowsmith, C.H. / Rico, M.
History
DepositionJun 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein MTH677


Theoretical massNumber of molelcules
Total (without water)10,5351
Polymers10,5351
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 34structures with the least restraint violations
RepresentativeModel #22lowest energy

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Components

#1: Protein Hypothetical protein MTH677 / Hypothesis


Mass: 10534.647 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: mth677 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O26773

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1224D-13C-separated NOESY
1313D 15N-separated NOESY
141HNHB

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM U-15N protein, 25mM sodium phosphate buffer pH 7.0, 450mM NaCl, 10mM DTT, 20uM ZnCl2, 1mM benzamidine, 90% H2O, 10% D2O90% H2O/10% D2O
21.0mM U-15N,13C protein, 25mM sodium phosphate buffer pH 7.0, 450mM NaCl, 10mM DTT, 20uM ZnCl2, 1mM benzamidine, 100% D2O100% D2O
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
NMRPipe2.2Delaglioprocessing
NMRView4Johnsondata analysis
CYANA1.0.5Guentertstructure solution
Amber7UCSFrefinement
RefinementMethod: distance geometry plus molecular mechanics / Software ordinal: 1
Details: NOE derived distance constraints: 1020, Hydrogen bond constraints: 44, Angle constraints: 165
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 34 / Conformers submitted total number: 30

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