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- PDB-2joq: Solution Structure of Protein HP0495 from H. pylori; Northeast st... -

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Basic information

Entry
Database: PDB / ID: 2joq
TitleSolution Structure of Protein HP0495 from H. pylori; Northeast structural genomics consortium target PT2; Ontario Centre for Structural Proteomics target HP0488
ComponentsHypothetical protein HP_0495
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HP0495 / non-uniform sampling / ABACUS / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homologyUncharacterised protein family UPF0250, YbeD-like / YbeD-like domain superfamily / Protein of unknown function (DUF493) / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein HP_0495
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsGutmanas, A. / Lemak, A. / Yee, A. / Karra, M. / Srisailam, S. / Semesi, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
Citation
Journal: To be Published
Title: Solution Structure of Protein HP0495 from H. pylori
Authors: Gutmanas, A. / Lemak, A. / Yee, A. / Karra, M. / Srisailam, S. / Semesi, A. / Arrowsmith, C.H.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionMar 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 18, 2012Group: Database references
Revision 1.4Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.7May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein HP_0495


Theoretical massNumber of molelcules
Total (without water)10,6731
Polymers10,6731
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical protein HP_0495


Mass: 10673.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP0495 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (gold) / References: UniProt: O25237

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO sparse
1513D HNCA sparse
1613D H(CCCO)NH-TOCSY sparse
1713D (H)C(CCO)NH-TOCSY
1814D HBHACBCA(CO)NH PR
1914D HC(CCO)NH-TOCSY PR
11013D 1H-15N NOESY sparse
11113D 1H-13C NOESY aliphatic
11223D H(C)CH-TOCSY sparse
11323D (H)CCH-TOCSY sparse
11413D 1H-13C NOESY aromatic
11523D 1H-13C NOESY sparse
11623D H(C)CH-TOCSY aromatic, sparse
11723D (H)CCH-TOCSY aromatic
11822D CT 1H-13C HSQC
11922D CT 1H-13C HSQC aromatic
NMR detailsText: Both 4D experiments were collected as 2D projection planes and processed with PR experiments marked "sparse" were collected with non-uniform sampling and processed with MDD

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMHP0495[U-13C; U-15N]1
10 mMTRIS1
300 mMsodium chloride1
1 mMbenzamidine1
10 mMDTT1
0.01 %sodium azide1
0.5 mMHP0495[U-13C; U-15N]2
10 mMTRIS2
300 mMsodium chloride2
1 mMbenzamidine2
10 mMDTT2
0.01 %sodium azide2
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003
Varian INOVAVarianINOVA5004

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdihedral angle constraints prediction
ABACUSA. Lemak, A. Grishaev, M. Llinas, CH Arrowsmithchemical shift and noe assignment
MDD/MDDguiA. Gutmanas, CH Arrowsmith, I Ibraghimov, V Yu Orekhovprocessing of non-uniformly sampled data
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PRM Karra, CH Arrowsmithprocessing of projection-reconstruction spectra
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: water refinement with CNS
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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