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- PDB-1wcj: Conserved Hypothetical Protein TM0487 from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1wcj
TitleConserved Hypothetical Protein TM0487 from Thermotoga maritima
ComponentsHYPOTHETICAL PROTEIN TM0487
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / CONTAINS PAAD DOMAIN / SIMILAR TO PAAD PROTEIN / UNKNOWN ACTIVITY / ALPHA/BETA FOLD / JCSG / HYPOTHETICAL PROTEIN / PSI / PROTEIN STRUCTURE INITIATIVE / JOINT CENTER FOR STRUCTURAL GENOMICS
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
Model type detailsMINIMIZED AVERAGE
AuthorsAlmeida, M.S. / Peti, W. / Herrmann, T. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
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
DepositionNov 17, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1May 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_software
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_software.name

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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)1 / 20LOWEST R.M.S.D. TO THE MEAN STRUCTURE
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
Details: CONFORMER WITH THE LOWEST R.M.S.D. TO THE MEAN STRUCTURE.
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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: IT REPRESENTS THE CLOSEST CONFORMER TO THE MEAN.. THE SAMPLE WAS 13C AND 15N-LABELED.

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Sample preparation

DetailsContents: 90% H2O/10% D2O, 20 MM SODIUM PHOSPHATE
Sample conditionspH: 6 / Pressure: 1 atm / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / 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: THIS STRUCTURE WAS ENERGY-MINIMIZED IN A WATER SHELL USING THE AMBER FORCE FIELD.
NMR ensembleConformer selection criteria: LOWEST R.M.S.D. TO THE MEAN STRUCTURE
Conformers calculated total number: 20 / Conformers submitted total number: 1

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