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- PDB-1zg2: Solution NMR structure of the UPF0213 protein BH0048 from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 1zg2
TitleSolution NMR structure of the UPF0213 protein BH0048 from Bacillus halodurans. Northeast Structural Genomics target BhR2.
ComponentsHypothetical UPF0213 protein BH0048
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / BhR2 / Autostructure / Northeast Structural Genomics Consortium / PSI / Protein Structure Initiative / NESG
Function / homologyGIY-YIG endonuclease / GIY-YIG endonuclease / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / 3-Layer(aba) Sandwich / Alpha Beta / UPF0213 protein BH0048
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAramini, J.M. / Swapna, G.V.T. / Xiao, R. / Ma, L. / Shastry, R. / Ciano, M. / Acton, T.B. / Liu, J. / Rost, B. / Cort, J.R. ...Aramini, J.M. / Swapna, G.V.T. / Xiao, R. / Ma, L. / Shastry, R. / Ciano, M. / Acton, T.B. / Liu, J. / Rost, B. / Cort, J.R. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the UPF0213 protein BH0048 from Bacillus halodurans. Northeast Structural Genomics target BhR2.
Authors: Aramini, J.M. / Swapna, G.V.T. / Xiao, R. / Ma, L. / Shastry, R. / Ciano, M. / Acton, T.B. / Liu, J. / Rost, B. / Cort, J.R. / Kennedy, M.A. / Montelione, G.T.
History
DepositionApr 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 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_software ...database_2 / pdbx_nmr_software / 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_software.name / _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: Hypothetical UPF0213 protein BH0048


Theoretical massNumber of molelcules
Total (without water)12,5561
Polymers12,5561
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 56structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical UPF0213 protein BH0048


Mass: 12556.251 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Plasmid: BhR2-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21MGK / References: UniProt: Q9KGL3

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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
1323D 13C-separated NOESY
141HNHA
153high resolution CH-HSQC
161backbone TR expts, TOCSYs, (H)CCH COSY
NMR detailsText: The structure was determined using triple resonance NMR spectroscopy. Partial automated backbone assignments were made using AUTOASSIGN, and the assignments were completed manually. Automatic ...Text: The structure was determined using triple resonance NMR spectroscopy. Partial automated backbone assignments were made using AUTOASSIGN, and the assignments were completed manually. Automatic NOESY assignments as well as distance and hydrogen bond constraints were determined using AUTOSTRUCTURE. Dihedral angle constraints were determined using HYPER and Talos. Completeness of NMR assignments (excluding N- and C-tags): backbone, 98%; side chain, 86%, aromatics, 100%; stereospecific methyl, 100%. Final structure quality factors (excluding the tags), where ordered residues [S(PHI) + S(PSI) > 1.8] comprise 7-16,19-25,27-38,51-85: (A) RMSD (6-30,48-86): BB 1.0; heavy atom, 1.6. FindCore RMSD: BB, 0.63; heavy atom, 0.86. (B) Ramachandran statistics for ordered residues: most favored, 96.7%, additionally allowed, 3.3%, generously allowed, 0.0%, disallowed, 0.0%. (C) Procheck scores for ordered residues (Raw/Z-): Phi-Psi, 0.02/0.39; All, -0.10/-0.59. (D) MolProbity clash score (Raw/Z-): 24.24/-2.63. (E) RPF scores for goodness of fit to NOESY data: F-measure, 0.916; Recall, 0.922; Precision, 0.910; DP-score, 0.663.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.67 mM U-13C,15N BhR2, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.55% D2O/95% H2O
20.67 mM U-13C,15N BhR2, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5100% D2O
30.56 mM U-15N,5% 13C BhR2, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.55% D2O/95% H2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 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 AVANCEBrukerAVANCE5001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA7504

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5pl6Brukercollection
VNMR6.1CVariancollection
NMRPipe2.3Delaglio et al.processing
Sparky3.91Goddard & Knellerdata analysis
AutoAssign1.15Zimmerman, Moseley, Montelionedata analysis
AutoStructure2.1.0Huang, Montelionerefinement
XPLOR-NIH2.0.6Clore et al.refinement
CNS1.1Brunger et al.refinement
PdbStat3.25Tejero & Montelionedata analysis
PSVS1Bhattacharya & Montelionedata analysis
FindCore1Snyder & Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 835 conformationally-restricting NOE-derived distance constraints, 250 dihedral angle constraints, and 52 hydrogen bond constraints (12.2 constraints ...Details: The structures are based on a total of 835 conformationally-restricting NOE-derived distance constraints, 250 dihedral angle constraints, and 52 hydrogen bond constraints (12.2 constraints per residue excluding tags; 2.9 long range constraints per residue). Structure determination was performed iteratively using AUTOSTRUCTURE (Xplor). The 10 lowest energy structures were further refined by restrained molecular dyanmics/energy minimization in explicit water (CNS). The unstructured N- (MAGDP) and C- (LEHHHHHH) terminal tags were included in all calculations but have been omitted from this deposition.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 56 / Conformers submitted total number: 10

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