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- PDB-1tvi: Solution structure of TM1509 from Thermotoga maritima: VT1, a NES... -

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Basic information

Entry
Database: PDB / ID: 1tvi
TitleSolution structure of TM1509 from Thermotoga maritima: VT1, a NESGC target protein
ComponentsHypothetical UPF0054 protein TM1509
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha + beta / mixed 4-stranded beta sheet / four helix bundle / Protein Structure Initiative / NESGC / PSI / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


RNA endonuclease activity / metalloendopeptidase activity / rRNA processing / Hydrolases; Acting on ester bonds / zinc ion binding / cytoplasm
Similarity search - Function
Metalloproteases ("zincins"), catalytic domain / Endoribonuclease YbeY, conserved site / Uncharacterized protein family UPF0054 signature. / Endoribonuclease YbeY / Metalloprotease catalytic domain superfamily, predicted / Endoribonuclease YbeY / Collagenase (Catalytic Domain) / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease YbeY
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / DYANA 1.5 with 30,000 TAD steps, simulated annealing
AuthorsPenhoat, C.H. / Atreya, H.S. / Kim, S. / Li, Z. / Yee, A. / Xiao, R. / Murray, D. / Arrowsmith, C.H. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2005
Title: NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure.
Authors: Penhoat, C.H. / Li, Z. / Atreya, H.S. / Kim, S. / Yee, A. / Xiao, R. / Murray, D. / Arrowsmith, C.H. / Szyperski, T.
History
DepositionJun 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 UPF0054 protein TM1509


Theoretical massNumber of molelcules
Total (without water)20,1581
Polymers20,1581
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 #1lowest target function

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Components

#1: Protein Hypothetical UPF0054 protein TM1509


Mass: 20157.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1509 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1J7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
133gNhsqc
1413D HNCO, 3D HN(CA)CB, 3D HabCab(CO)NH, 3D HNCAHA, 3D HCCHCOSY (C13,1H,1H), 3D HCCHTOCSY (13C,13C,1H)
152CT gChsqc 2D spectra
NMR detailsText: Both aliphatic and aromatic 3D_13C-separated_NOESY were conducted

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM TM1509 (100% 15N, 100% 13C), 450 mM NaCl, 25 mM NaHPO4, 10mM DTT, 0.01% NaN3, 1mM benzamidine, 1 x inhibitor cocktail pill, 95% H2O, 5% D2O95% H2O/5% D2O
21.2 mM TM1509 (100% 15N, 5% 13C), 450 mM NaCl, 25 mM NaHPO4, 10mM DTT, 0.01% NaN3, 1mM benzamidine, 1 x inhibitor cocktail pill, 95% H2O, 5% D2O95% H2O/5% D2O
31.2 mM TM1509 (100% 15N, 5% 13C), 450 mM NaCl, 25 mM NaHPO4, 10mM DTT, 0.01% NaN3, 1mM benzamidine, 1 x inhibitor cocktail pill, 95% H2O/5% D20 was titrated with D20 to reveal slowly exchanging amide protons95% H2O/5% D20 was titrated with D20 to reveal slowly exchanging amide protons
Sample conditionspH: 6.5 / Pressure: 1.0 atmosphere atm / Temperature: 298 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
DYANA1.5Guntert, Mumenthaler, Wuthrichstructure solution
CYANA1.05Hermann, Guntert, Wuthrichrefinement
MOLMOL1Koradi, R.; Billeter, M.; Wuthrich, K.data analysis
XEASY1.3.3Bartels, C.; Billeter, M.; Guntert, P.; Wuthrich, K.;data analysis
TALOS98.040.21.02Cornilescu, G.; Delaglio, F.; Bax, A.data analysis
RefinementMethod: DYANA 1.5 with 30,000 TAD steps, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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