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- PDB-2hga: Solution NMR Structure of Conserved protein MTH1368, Northeast St... -

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Basic information

Entry
Database: PDB / ID: 2hga
TitleSolution NMR Structure of Conserved protein MTH1368, Northeast Structural Genomics Consortium Target TT821A
ComponentsConserved protein MTH1368
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved protein MTH1368 / GFT NMR / PSI / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / Hydrolase / Metal-binding / Metalloprotease / Protease / Transmembrane / Zinc b
Function / homology
Function and homology information


metalloendopeptidase activity / membrane => GO:0016020
Similarity search - Function
Membrane-bound transcription factor site-2 protease / Peptidase M50 / Peptidase family M50 / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...Membrane-bound transcription factor site-2 protease / Peptidase M50 / Peptidase family M50 / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsLiu, G. / Lin, Y. / Parish, D. / Shen, Y. / Sukumaran, D. / Yee, A. / Semesi, A. / Arrowsmith, C. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: Solution NMR Structure of Conserved protein MTH1368, Northeast Structural Genomics Consortium Target TT821A
Authors: Liu, G. / Lin, Y. / Parish, D. / Shen, Y. / Sukumaran, D. / Yee, A. / Semesi, A. / Arrowsmith, C. / Szyperski, T.
History
DepositionJun 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 29, 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: Conserved protein MTH1368


Theoretical massNumber of molelcules
Total (without water)13,4031
Polymers13,4031
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Conserved protein MTH1368


Mass: 13402.898 Da / Num. of mol.: 1 / Fragment: Residues 208-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: MTH1368, MTH_1368 / Plasmid: MTH1368_208_310 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold magic / References: UniProt: O27421

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111SIMULTANEOUS HETERONUCLEAR RESOLVED [1H,1H]-NOESY
1213D HN(CA)CB
1313D CBCA(CO)NH
141GFT (4,3)D HABCAB(CO)NHN
151GFT (4,3)D (H)CCH

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Sample preparation

DetailsContents: U-15N,13C; TRIS BUFFER, PH7.0, 200 mM NaCl2, ~10 uM ZnSO4, 0.01% NaN3, 1mM bezamidine, 1x inhibitor, 93% H2O, 7% D2O.
Solvent system: 93% H2O/7% D2O
Sample conditionspH: 7 / Pressure: ambient / Temperature: 288 K

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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 INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe2.3Delaglio, F.processing
AutoAssign1.15.1MOSELEY, H.data analysis
AutoStructure2HUANG, Y.J.data analysis
CYANA2.1GUNTERTstructure solution
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARRENrefinement
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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