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- PDB-1iio: NMR-Based Structure of the Conserved Protein MTH865 from the Arch... -

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Basic information

Entry
Database: PDB / ID: 1iio
TitleNMR-Based Structure of the Conserved Protein MTH865 from the Archea Methanobacterium thermoautotrophicum
Componentsconserved hypothetical protein MTH865
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / 4-helical bundle / monomer
Function / homologyMTH865-like / Uncharacterised protein family MTH865 / MTH865-like superfamily / MTH865-like family / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha / Conserved protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsLee, G.M. / Edwards, A.M. / Arrowsmith, C.H. / McIntosh, L.P.
CitationJournal: J.Biomol.NMR / Year: 2001
Title: NMR-based structure of the conserved protein MTH865 from the archaeon Methanobacterium thermoautotrophicum.
Authors: Lee, G.M. / Edwards, A.M. / Arrowsmith, C.H. / McIntosh, L.P.
History
DepositionApr 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein MTH865


Theoretical massNumber of molelcules
Total (without water)8,6821
Polymers8,6821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein conserved hypothetical protein MTH865


Mass: 8681.726 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Species: Methanothermobacter thermautotrophicusMethanothermobacter
Strain: delta H / Gene: ORF 865 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q04926

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1224D 13C/15N-separated NOESY
1332D NOESY
2423D 13C-separated methyl-methyl NOESY
NMR detailsText: The backbone and sidechain chemical shifts were assigned manually using standard 3D heternuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM MTH865 U-15N; 50mM PO4 buffer, 50mM NaCl, 5mM DTT, 3mM NaN390% H2O/10% D2O
20.5mM MTH865 U-15N,13C; 50mM PO4 buffer, 50mM NaCl, 5mM DTT, 3mM NaN390% H2O/10% D2O
30.5mM MTH865 U-15N,10%-13C; 50mM PO4 buffer, 50mM NaCl, 5mM DTT, 3mM NaN399% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl 6.51 ambient 303 K
250mM NaCl 6.51 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bVarian, Inc.collection
Felix95.0 and 2000Molecular Simulations, Inc.processing
Felix95.0 and 2000Molecular Simulations, Inc.data analysis
ARIA/CNS1Nilges, M. (ARIA); Brunger, A. (CNS)structure solution
ARIA/CNS1Nilges, M. (ARIA); Brunger, A. (CNS)refinement
TALOS1Cornilescu, F., Delaglio, F., Bax, A.data analysis
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: 1492 UNAMBIGUOUS AND 544 AMBIGUOUS ARIA-DERIVED NOE RESTRAINTS (BASED ON 17 ITERATIONS) WERE USED FOR THE STRUCTURE CALCULATION AND REFINEMENT. 50 PAIRS OF PHI AND PSI DIHEDRAL ANGLE AND 26 ...Details: 1492 UNAMBIGUOUS AND 544 AMBIGUOUS ARIA-DERIVED NOE RESTRAINTS (BASED ON 17 ITERATIONS) WERE USED FOR THE STRUCTURE CALCULATION AND REFINEMENT. 50 PAIRS OF PHI AND PSI DIHEDRAL ANGLE AND 26 PAIRS OF HYDROGEN-BOND RESTRAINTS WERE ALSO INCLUDED IN THE CALCULATIONS. DIHEDRAL ANGLE RESTRAINTS WERE CALCULATED USING TALOS, WHILE HYDROGEN BOND RESTRAINTS WERE DERIVED FROM A 15/1H-HSQC H2O-D2O EXCHANGE STUDY. THE STRUCTURE ENSEMBLE INCLUDES THREE ADDITIONAL RESIDUES AT THE N-TERMINUS (GLY-SER-HIS), RESULTING FROM THE PROTEOLYTIC CLEAVAGE OF A HIS6 AFFINITY TAG. RESIDUE NUMBERING BEGINS WITH GLY-3 AND ENDS WITH LEU81
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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