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- PDB-1rzw: The Solution Structure of the Archaeglobus fulgidis protein AF209... -

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Basic information

Entry
Database: PDB / ID: 1rzw
TitleThe Solution Structure of the Archaeglobus fulgidis protein AF2095. Northeast Structural Genomics Consortium target GR4
ComponentsProtein AF2095(GR4)
KeywordsStructural Genomics / Unknown function / Beta-sheet of 4 parallel / anti-parallel beta-strands and 3 alpha-helices / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / translation / cytosol
Similarity search - Function
Peptidyl-tRNA hydrolase, archaea / Peptidyl-tRNA hydrolase, PTH2 / Peptidyl-tRNA hydrolase PTH2 / Bit1 / Bit1 / Peptidyl-tRNA hydrolase II domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
AuthorsPowers, R. / Acton, T.B. / Huang, Y.J. / Liu, J. / Ma, L. / Rost, B. / Chiang, Y. / Cort, J.R. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: Protein Sci. / Year: 2005
Title: Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes
Authors: Powers, R. / Mirkovic, N. / Goldsmith-Fischman, S. / Acton, T.B. / Chiang, Y. / Huang, Y.J. / Ma, L. / Rajan, P.K. / Cort, J.R. / Kennedy, M.A. / Liu, J. / Rost, B. / Honig, B. / Murray, D. / Montelione, G.T.
#1: Journal: J.Biomol.Nmr / Year: 2004
Title: 1H, 13C and 15N assignments for the Archaeglobus fulgidis protein AF2095.
Authors: Powers, R. / Acton, T.B. / Chiang, Y. / Paranji, R. / Cort, J.R. / Kennedy, M.A. / Liu, J. / Ma, L. / Rost, B. / Montelione, G.T.
History
DepositionDec 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _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: Protein AF2095(GR4)


Theoretical massNumber of molelcules
Total (without water)13,5791
Polymers13,5791
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 / -
Representative

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Components

#1: Protein Protein AF2095(GR4)


Mass: 13578.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF2095 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: O28185

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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
131HNHA
141triple-resonance experiments for backbone/sidechain assignments

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Sample preparation

DetailsContents: 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, 5% D2O pH 6.5
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3
pH: 6.5 / Pressure: ambient / Temperature: 313 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
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7502
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglioprocessing
XPLOR-NIH2.9.1Schwieters, Kuszewski, Tjandra, Clore, Brungerstructure solution
PIPP4.3.5Garrettdata analysis
AutoAssign1.11.1Zimmerman, Moseley, Kiriyevs,Kulikowski,Montelionedata analysis
AutoStructure2.0bHuang, Montelionerefinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR ensembleConformers submitted total number: 1

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