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- PDB-1xax: NMR structure of HI0004, a putative essential gene product from H... -

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Basic information

Entry
Database: PDB / ID: 1xax
TitleNMR structure of HI0004, a putative essential gene product from Haemophilus influenzae
ComponentsHypothetical UPF0054 protein HI0004
Keywordsstructural genomics / unknown function / Haemophilus influenzae / MMP / hydrolase / protein structure initiative / S2F / Structure 2 Function Project
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 speciesHaemophilus influenzae (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics
AuthorsYeh, D.C. / Parsons, J.F. / Parsons, L.M. / Liu, F. / Eisenstein, E. / Orban, J. / Structure 2 Function Project (S2F)
Citation
Journal: Protein Sci. / Year: 2005
Title: NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog
Authors: Yeh, D.C. / Parsons, L.M. / Parsons, J.F. / Liu, F. / Eisenstein, E. / Orban, J.
#1: Journal: J.Biomol.NMR / Year: 2004
Title: NMR assignment of the hypothetical protein HI0004 from Haemophilus Influenzae - a putative essential gene product
Authors: Yeh, D.C. / Parsons, J.F. / Parsons, L.M. / Liu, F. / Eisenstein, E. / Orban, J.
History
DepositionAug 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
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 HI0004


Theoretical massNumber of molelcules
Total (without water)17,3691
Polymers17,3691
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 least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Hypothetical UPF0054 protein HI0004


Mass: 17369.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P71335

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HN(CA)CB
141CBCA(CO)NH
151C(CO)NH
161H(CCO)NH
NMR detailsText: NH residual dipolar coupling were used for validation of structure

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Sample preparation

DetailsContents: 1mM U-15N,13C hi0004, 50mM phosphate buffer, 10mM NaCl
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM phosphate, 100mM NaCl / pH: 7 / Pressure: ambient / 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
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Clore, M.structure solution
CNS1.1Clore, M.refinement
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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