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Yorodumi- PDB-2kl3: Solution NMR structure of the Rhodanese-like domain from Anabaena... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kl3 | ||||||
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Title | Solution NMR structure of the Rhodanese-like domain from Anabaena sp Alr3790 protein. Northeast Structural Genomics Consortium Target NsR437A | ||||||
Components | Alr3790 protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha+beta / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc sp. (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Eletsky, A. / Belote, R.L. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Eletsky, A. / Belote, R.L. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Solution NMR structure of the Rhodanese-like domain from Anabaena sp Alr3790 protein. Northeast Structural Genomics Consortium Target NsR437A Authors: Eletsky, A. / Belote, R.L. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kl3.cif.gz | 895.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kl3.ent.gz | 763.8 KB | Display | PDB format |
PDBx/mmJSON format | 2kl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kl3_validation.pdf.gz | 342.9 KB | Display | wwPDB validaton report |
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Full document | 2kl3_full_validation.pdf.gz | 469.8 KB | Display | |
Data in XML | 2kl3_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 2kl3_validation.cif.gz | 66.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/2kl3 ftp://data.pdbj.org/pub/pdb/validation_reports/kl/2kl3 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14539.063 Da / Num. of mol.: 1 Fragment: Rhodanese-like domain sequence database residues 17-139 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr3790 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8YQN0 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Structure determination was performed iteratively with CYANA and AUTOSTRUCTURE using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, hydrogen bond constraints based ...Details: Structure determination was performed iteratively with CYANA and AUTOSTRUCTURE using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, hydrogen bond constraints based on preliminary structures and CLEANEX data, and RDCs from two alignment media. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 2802 / NOE intraresidue total count: 517 / NOE long range total count: 978 / NOE medium range total count: 633 / NOE sequential total count: 674 / Hydrogen bond constraints total count: 220 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 64 / Protein psi angle constraints total count: 64 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.12 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5.1 ° / Maximum upper distance constraint violation: 0.416 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.018 Å |