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Yorodumi- PDB-2kke: Solution NMR Structure of a dimeric protein of unknown function f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kke | ||||||
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Title | Solution NMR Structure of a dimeric protein of unknown function from Methanobacterium thermoautotrophicum, Northeast Structural Genomics Consortium Target TR5 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | Structural Genomics / Unknown function / Protein NMR / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / Target TR5 / PSI-2 / Protein Structure Initiative / Methanothermobacter thermautotrophicus / O26567_METTH / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Arc Repressor Mutant - #60 / Arc Repressor Mutant / Orthogonal Bundle / Mainly Alpha / CopG family transcriptional regulator Function and homology information | ||||||
Biological species | Methanothermobacter thermautotrophicus str. Delta H (archaea) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Swapna, G.V.T. / Gunsalus, X. / Huang, L. / Xiao, K. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: NMR Solution Structure of a putative uncharacterized protein from Methanobacterium thermoautotrophicum, Northeast Structural Genomics Consortium Target:TR5 Authors: Swapna, G.V.T. / Gunsalus, X. / Huang, L. / Xiao, K. / Everett, J.K. / Acton, T.B. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kke.cif.gz | 730.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kke.ent.gz | 619.7 KB | Display | PDB format |
PDBx/mmJSON format | 2kke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kke_validation.pdf.gz | 468.4 KB | Display | wwPDB validaton report |
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Full document | 2kke_full_validation.pdf.gz | 659.2 KB | Display | |
Data in XML | 2kke_validation.xml.gz | 36 KB | Display | |
Data in CIF | 2kke_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/2kke ftp://data.pdbj.org/pub/pdb/validation_reports/kk/2kke | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 5972.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea) Gene: MTH467, MTH_467 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: O26567 Sequence details | NMR ANALYSIS SHOWED THAT THE RESIDUE AT 53 AND 253 IS A GLU AND NOT AN ASP. THE DATABASE HAS TO BE ...NMR ANALYSIS SHOWED THAT THE RESIDUE AT 53 AND 253 IS A GLU AND NOT AN ASP. THE DATABASE HAS TO BE CORRECTED FOR THIS. GLU IS CORRECT. | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple resonance NMR spectroscopy. Automated backbone assignments were made using AutoAssign software. Sidechain assignments were completed manually. The ...Text: The structure was determined using triple resonance NMR spectroscopy. Automated backbone assignments were made using AutoAssign software. Sidechain assignments were completed manually. The oligomeric state was confirmed to be a dimer from sedimentation-equilibrium analysis (Kd =0.3uM) and static light scattering experiment that reported 90% of the protein in a dimer with a molecular weight of 15.03kD. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 300 mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Initial NOESY assignments for the monomer were made using AutoStructure and the solution structure of the dimer was obtained using CYANA-2.1. Constraints for the dimer interface were ...Details: Initial NOESY assignments for the monomer were made using AutoStructure and the solution structure of the dimer was obtained using CYANA-2.1. Constraints for the dimer interface were obtained from the x-filtered NOESY data and slow exchanging amides from H/D exchange. 100 structures were calculated and 20 best conformers were then refined in a shell of water using CNS. Initial dihedral angle constraints were obtained from TALOS. Final structure quality factors determined using PSVS software: ordered residues are defined as (10-53,212-236,238-251). (a)RMSD(ordered residues) all Backbone atoms: 0.7A; all heavy atoms: 1.0A. (b) Ramchandran statistics for all ordered residues: Most favoured region: 93.1%; Additionally allowed region: 6.6%; Generously allowed region 0.1% and disallowed region: 0.2%. (c) Procheck scores for all ordered residues (Raw/Z) phi-psi -0.11/-0.12; All: -0.07/-0.41; (d) MolProbity clash score (Raw/Z): 16.97/-1.39. (e) RPF scores for the goodness of fit to NOESY data: Recall :0.913; Precision:0.849; F-measure:0.88; Final DP score :0.703 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |