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- PDB-1eiw: Solution structure of hypothetical protein MTH538 from Methanobac... -

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Basic information

Entry
Database: PDB / ID: 1eiw
TitleSolution structure of hypothetical protein MTH538 from Methanobacterium thermoautotrophicum
ComponentsHYPOTHETICAL PROTEIN MTH538
KeywordsSTRUCTURAL GENOMICS / CheY-like fold / flavodoxin-like fold / (a/b)5 doubly wound fold / parallel beta sheet / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyHypothetical protein MTH538 / Thoeris protein ThsB, TIR-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Protein MTH_538
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsCort, J.R. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structure-based functional classification of hypothetical protein MTH538 from Methanobacterium thermoautotrophicum.
Authors: Cort, J.R. / Yee, A. / Edwards, A.M. / Arrowsmith, C.H. / Kennedy, M.A.
History
DepositionFeb 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: 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 1.4May 22, 2024Group: 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: HYPOTHETICAL PROTEIN MTH538


Theoretical massNumber of molelcules
Total (without water)12,3961
Polymers12,3961
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)16 / 20structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein HYPOTHETICAL PROTEIN MTH538


Mass: 12395.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: O26638

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1124D 13C-separated NOESY
1233D 15N-separated NOESY
133HMQC-J
1413D 13C,15N-simultaneous NOESY
1541H-15N HSQC D2O exchange

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM MTH538 U-15N,13C; 25 mM phosphate buffer pH 7.4, 150 mM NaCl, 90% H2O, 10% D2O, 5 mM DTT90% H2O/10% D2O
22mM MTH538 U-15N,13C; 25 mM phosphate buffer pH 7.1, 150 mM NaCl, 99% D2O, 5 mM DTT99% D2O
32mM MTH538 U-15N; 25 mM phosphate buffer pH 7.4, 150 mM NaCl, 90% H2O, 10% D2O, 5 mM DTT90% H2O/10% D2O
42mM MTH538 U-15N; 25 mM phosphate buffer pH 7.1, 150 mM NaCl, 99% D2O, 5 mM DTT99% D2O
Sample conditionsIonic strength: 150 mM salt, 25 mM phosphate buffer / pH: 7.4 / 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
Varian INOVAVarianINOVA6001
Varian UNITYPLUSVarianUNITYPLUS5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
Felix98MSIprocessing
VNMRVariancollection
X-PLOR3.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: 519 NOE-derived distance constraints 55 dihedral angle constraints (phi) 28 hydrogen bonds (2 constraints per H-bond)
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 16

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