[English] 日本語
Yorodumi- PDB-2lzz: Solution structure of a mutant of the triheme cytochrome PpcA fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lzz | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of a mutant of the triheme cytochrome PpcA from Geobacter sulfurreducens sheds light on the role of the conserved aromatic residue F15 | ||||||
Components | Cytochrome c, 3 heme-binding sites | ||||||
Keywords | ELECTRON TRANSPORT / Geobacter / Triheme cytochrome / Site-directed mutagenesis | ||||||
Function / homology | Cytochrome C3 / Cytochrome C3 / Alpha-Beta Complex / Alpha Beta / PROTOPORPHYRIN IX CONTAINING FE / : Function and homology information | ||||||
Biological species | Geobacter sulfurreducens (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Dantas, J.M. / Morgado, L. / Turner, D.L. / Salgueiro, C.A. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Solution structure of a mutant of the triheme cytochrome PpcA from Geobacter sulfurreducens sheds light on the role of the conserved aromatic residue F15. Authors: Dantas, J.M. / Morgado, L. / Pokkuluri, P.R. / Turner, D.L. / Salgueiro, C.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2lzz.cif.gz | 463.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2lzz.ent.gz | 401.8 KB | Display | PDB format |
PDBx/mmJSON format | 2lzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lzz_validation.pdf.gz | 636.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2lzz_full_validation.pdf.gz | 770.1 KB | Display | |
Data in XML | 2lzz_validation.xml.gz | 49 KB | Display | |
Data in CIF | 2lzz_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/2lzz ftp://data.pdbj.org/pub/pdb/validation_reports/lz/2lzz | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 7714.133 Da / Num. of mol.: 1 / Mutation: F15L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: DL-1 / KN400 / Gene: GSU0612, KN400_0591, ppcA / Plasmid: pCK32 / Production host: Escherichia coli (E. coli) / References: UniProt: D7AFU0 |
---|---|
#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||
Sample conditions |
|
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz |
---|
-Processing
NMR software |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1822 / NOE intraresidue total count: 704 / NOE long range total count: 453 / NOE medium range total count: 300 / NOE sequential total count: 365 | |||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.27 Å / Maximum upper distance constraint violation: 0.26 Å | |||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 1.14 Å / Distance rms dev error: 0.1 Å |