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- PDB-1iqs: Minimized average structure of MTH1880 from Methanobacterium Ther... -

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Basic information

Entry
Database: PDB / ID: 1iqs
TitleMinimized average structure of MTH1880 from Methanobacterium Thermoautotrophicum
ComponentsMTH1880
KeywordsMETAL BINDING PROTEIN / alpha-beta / anti-parallel
Function / homologyHypothetical protein MTH1880 / Protein of unknown function DUF749 / Uncharacterised conserved protein UCP005648, calcium-binding / Hypothetical protein MTH1880 / Domain of unknown function (DUF749) / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / Conserved protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics matrix relaxation torsion angle dynamics
Model type detailsminimized average
AuthorsLee, C.H. / Shin, J. / Bang, E. / Jung, J.W. / Yee, A. / Arrowsmith, C.H. / Lee, W.
CitationJournal: Protein Sci. / Year: 2004
Title: Solution structure of a novel calcium binding protein, MTH1880, from Methanobacterium thermoautotrophicum.
Authors: Lee, C.H. / Jung, J.W. / Yee, A. / Arrowsmith, C.H. / Lee, W.
History
DepositionJul 29, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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: MTH1880


Theoretical massNumber of molelcules
Total (without water)9,9601
Polymers9,9601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1This model is the minimized average structure from 20 structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein MTH1880 / conserved protein


Mass: 9960.412 Da / Num. of mol.: 1 / Mutation: M1L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Plasmid: pET13b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: O27908

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
132HNHA
1432D 15N HSQC for H/D exchange
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM MTH1880 U-15N,13C; 25mM phosphate buffer, 300mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
22mM MTH1880 U-15N; 25mM phosphate buffer, 300mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
31mM MTH1880 U-15N; 25mM phosphate buffer, 300mM NaCl; 100% D2O100% D2O
Sample conditionspH: 7.6 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Inc.collection
VNMR6.1BVarian Inc.collection
NMRPipe1.8Delaglioprocessing
Sparky3.98Jamesdata analysis
CNS1Brungerrefinement
Insight II2000MSI Inc.structure solution
MOLMOL2.6.0Wuthrichstructure solution
RefinementMethod: distance geometry simulated annealing, molecular dynamics matrix relaxation torsion angle dynamics
Software ordinal: 1
Details: the structures are based on a total of 762 restraints, 669 are NOE-derived distance constraints, 39 dihedral angle restraints,54 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: This model is the minimized average structure from 20 structures with the lowest energy
Conformers calculated total number: 1 / Conformers submitted total number: 1

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