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- PDB-1uwd: NMR STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM THERMOTOGA ... -

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Basic information

Entry
Database: PDB / ID: 1uwd
TitleNMR STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM THERMOTOGA MARITIMA (TM0487), WHICH BELONGS TO THE DUF59 FAMILY.
ComponentsHYPOTHETICAL PROTEIN TM0487
KeywordsBIOSYNTHETIC PROTEIN / SIMILAR TO PAAD PROTEIN / ALPHA/BETA FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology: / Fe-S cluster assembly (FSCA) / MIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / MIP18 family-like domain-containing protein
Function and homology information
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodSOLUTION NMR / distance geometry
AuthorsAlmeida, M.S. / Peti, W. / Herrmann, T. / Wuthrich, K.
Citation
Journal: Protein Sci. / Year: 2005
Title: NMR Structure of the Conserved Hypothetical Protein Tm0487 from Thermotoga Maritima: Implications for 216 Homologous Duf59 Proteins.
Authors: Almeida, M.S. / Herrmann, T. / Peti, W. / Wilson, I.A. / Wuthrich, K.
#1: Journal: J.Biomol.NMR / Year: 2004
Title: 1H-, 13C- and 15N-NMR Assignment of the Conserved Hypothetical Protein Tm0487 from Thermotoga Maritima
Authors: Almeida, M.S. / Peti, W. / Wuthrich, K.
History
DepositionFeb 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: pdbx_database_related / pdbx_nmr_software
Item: _pdbx_database_related.db_name / _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN TM0487


Theoretical massNumber of molelcules
Total (without water)11,5171
Polymers11,5171
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 / 100
Representative

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Components

#1: Protein HYPOTHETICAL PROTEIN TM0487


Mass: 11517.340 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9WYV7
Sequence detailsMET 1 AND PRO 2 ARE NOT INCLUDED IN THESE STRUCTURES. THE MET1 IS NOT PRESENT IN THE RECOMBINANT PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-RESOLVED [1H
1211H]-NOESY
1313D 13C-RESOLVED [1H
1411H]-NOESY
NMR detailsText: THE SAMPLE WAS 13C AND 15N-LABELED.

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Sample preparation

DetailsContents: 90% H2O/10% D2O, 20MM SODIUM PHOSPHATE
Sample conditionspH: 6 / Pressure: 1 atm / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
OPALpR.KORADI,M.BILLETER,P.GUNTERTrefinement
ATNOS/Cstructure solution
ID/DYANAstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: THESE STRUCTURES WERE ENERGY- MINIMIZED IN A WATER SHELL USING THE AMBER FORCE FIELD. 20 LOWEST ENERGY NMR STRUCTURES. THESE STRUCTURES WERE FITTED BY MOLMOL.
NMR ensembleConformers calculated total number: 100 / Conformers submitted total number: 20

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