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Yorodumi- PDB-2klb: NMR Solution structure of a diflavin flavoprotein A3 from Nostoc ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2klb | ||||||
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Title | NMR Solution structure of a diflavin flavoprotein A3 from Nostoc sp. PCC 7120, Northeast Structural Genomics Consortium Target NsR431C | ||||||
Components | Putative diflavin flavoprotein A 3 | ||||||
Keywords | OXIDOREDUCTASE / PSI-2 / NESG / NsR431C / protein NMR / Q8YQD8 / Electron transport / Iron / Metal-binding / Transport / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / Oxidoreductases / FMN binding / metal ion binding Similarity search - Function | ||||||
Biological species | Nostoc sp. (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Swapna, G.V.T. / Ciccosanti, C. / Wang, D. / Jiang, M. / Xiao, R. / Acton, T.B. / Everett, J.K. / Nair, R. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: NMR Solution structure of a diflavin flavoprotein A3 from Nostoc sp. PCC 7120, Northeast Structural Genomics Consortium Target NsR431C Authors: Swapna, G.V.T. / Ciccosanti, C. / Wang, D. / Jiang, M. / Xiao, R. / Acton, T.B. / Everett, J.K. / Nair, R. / 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 | 2klb.cif.gz | 994.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2klb.ent.gz | 838.9 KB | Display | PDB format |
PDBx/mmJSON format | 2klb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2klb_validation.pdf.gz | 470.6 KB | Display | wwPDB validaton report |
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Full document | 2klb_full_validation.pdf.gz | 642.1 KB | Display | |
Data in XML | 2klb_validation.xml.gz | 69.4 KB | Display | |
Data in CIF | 2klb_validation.cif.gz | 85 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/2klb ftp://data.pdbj.org/pub/pdb/validation_reports/kl/2klb | 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: 16475.482 Da / Num. of mol.: 1 / Fragment: Flavodoxin-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: all3895, dfa3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q8YQD8 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Data acquisition on B600 was performed using 35ul of 1.18mM sample and a 1.7mm microcryoprobe. The structure was determined using triple resonance NMR spectroscopy. Automated backbone ...Text: Data acquisition on B600 was performed using 35ul of 1.18mM sample and a 1.7mm microcryoprobe. The structure was determined using triple resonance NMR spectroscopy. Automated backbone assignments were made using AutoAssign. Sidechain assignments were completed manually. Automated NOESY assignments were made using AutoStructure and structure solution was determined using AutoStructure and CYANA-2.1. The structure calculations were done including the C-terminal 6xHis tag LEHHHHHH. Resonance assignments were validated using AVS validation software. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 5mM CaCl2, 200mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: 140 structures were calculated and 20 best conformers were refined in a shell of water using CNS. Initial dihedral angles were obtained using TALOS. Final quality scores were determined ...Details: 140 structures were calculated and 20 best conformers were refined in a shell of water using CNS. Initial dihedral angles were obtained using TALOS. Final quality scores were determined using PSVS software. Ordered residues are defined as: 2 - 9, 12 - 27, 31 - 36, 40 - 57, 61 - 79, 84 - 85, 87 - 89, 96 - 108, 110 - 111, 122 - 146; (a) RMSD (ordered residues) all Backbone atoms: 1.0A; all heavy atoms: 1.4A; (b) Ramachandran statistics for all ordered residues: Most favoured: 92.1%; Additionally allowed: 7.2%; Generously allowed: 0.6%; disallowed: 0.2%; (c) Procheck scores for ordered residues (Raw/Z)phi-psi -0.04/0.16, All:-0.10/-0.59. (d) MolProbity clash score (Raw/Z) 22.23/-2.12. | ||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1672 / NOE intraresidue total count: 134 / NOE long range total count: 565 / NOE medium range total count: 481 / NOE sequential total count: 492 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 140 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 8.5 Å / Maximum upper distance constraint violation: 11.6 Å | ||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.09 Å / Distance rms dev error: 0.09 Å |