[English] 日本語
Yorodumi- PDB-2dvh: THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dvh | ||||||
---|---|---|---|---|---|---|---|
Title | THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES | ||||||
Components | CYTOCHROME C-553 | ||||||
Keywords | ELECTRON TRANSPORT / CYTOCHROME C / HEME | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS ENERGY REFINEMENT | ||||||
Authors | Sebban-Kreuzer, C. / Blackledge, M.J. / Dolla, A. / Marion, D. / Guerlesquin, F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Structure and dynamics of ferrocytochrome c553 from Desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics. Authors: Blackledge, M.J. / Medvedeva, S. / Poncin, M. / Guerlesquin, F. / Bruschi, M. / Marion, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dvh.cif.gz | 911.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dvh.ent.gz | 798.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/2dvh ftp://data.pdbj.org/pub/pdb/validation_reports/dv/2dvh | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 8225.436 Da / Num. of mol.: 1 / Mutation: Y64A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria) Species: Desulfovibrio vulgaris / Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / Cellular location: PERIPLASM / Gene: M13CYF / Plasmid: PRC41/TYR64ALA / Cellular location (production host): PERIPLASM / Gene (production host): CYF / Production host: Desulfovibrio desulfuricans (bacteria) / Strain (production host): G200 / References: UniProt: P04032 |
---|---|
#2: Chemical | ChemComp-HEC / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Sample conditions | pH: 5.9 / Temperature: 310 K |
---|---|
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz |
---|
-Processing
Software | Name: AMBER / Classification: refinement | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR software |
| ||||||||||||
Refinement | Method: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS ENERGY REFINEMENT Software ordinal: 1 | ||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 40 / Conformers submitted total number: 39 |