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- PDB-2akl: Solution structure for phn-A like protein PA0128 from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 2akl
TitleSolution structure for phn-A like protein PA0128 from Pseudomonas aeruginosa
ComponentsphnA-like protein pa0128
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two domains / Zn binding protein / Beta-strand protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


Protein YjdM, N-terminal / PhnA Zinc-Ribbon / Protein YjdM / Protein YjdM, C-terminal / PhnA domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / SH3 Domains / Single Sheet / SH3 type barrels. ...Protein YjdM, N-terminal / PhnA Zinc-Ribbon / Protein YjdM / Protein YjdM, C-terminal / PhnA domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / SH3 Domains / Single Sheet / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSrisailam, S. / Yee, A. / Lemak, A. / Lukin, J.A. / Bansal, S. / Prestegard, J.H. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: J.Biomol.Nmr / Year: 2006
Title: Sequence Specific Resonance Assignment of a Hypothetical Protein PA0128 from Pseudomonas Aeruginosa
Authors: Srisailam, S. / Lukin, J.A. / Lemak, A. / Yee, A. / Arrowsmith, C.H.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: phnA-like protein pa0128
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0582
Polymers14,9931
Non-polymers651
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein phnA-like protein pa0128 / hypothetical protein PA0128


Mass: 14992.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PAO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I704
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
133J MODULATED HSQC for RDC

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Sample preparation

DetailsContents: 1mM pa0128, U-15N,13C: 400 mM NaCl, 20 mM Na2PO4, 1 mM Benzamidine, 15 mM DTT, 20 uM ZnSO4, 0.01% NAN3, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 400 mM NaCl, 20 mM Phosphate buffer / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, F.processing
Sparky3.106Goddard,T.D. and Kneller,D. G.data analysis
CYANA2.1Gunter, P.structure solution
CNS1.1Brunger, A. T. et alrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 2448 NOE derived distance restraints, 132 torsion angle restraints, 62 RDC restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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