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Yorodumi- PDB-5zkv: Solution structure of molten globule state of L94G mutant of hors... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zkv | ||||||
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Title | Solution structure of molten globule state of L94G mutant of horse cytochrome-c | ||||||
Components | Cytochrome c | ||||||
Keywords | ELECTRON TRANSPORT / Structure from MOLMOL | ||||||
Function / homology | Function and homology information cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process ...cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process / apoptotic process / lipid binding / heme binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Authors | Naiyer, A. / Islam, A. / Hassan, M.I. / Sundd, M. / Ahmad, F. | ||||||
Citation | Journal: To Be Published Title: Solution structure of molten globule state of L94G mutant of horse cytochrome-c Authors: Naiyer, A. / Islam, A. / Hassan, M.I. / Sundd, M. / Ahmad, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zkv.cif.gz | 505.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zkv.ent.gz | 422.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/5zkv ftp://data.pdbj.org/pub/pdb/validation_reports/zk/5zkv | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11669.492 Da / Num. of mol.: 1 / Mutation: L94G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: CYCS, CYC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: P00004 |
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#2: Chemical | ChemComp-HEC / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 2 mM [U-99% 13C; U-99% 15N] Molten globule of L94G mutant of horse cytochrome-c, 90% H2O/10% D2O Details: NMR sample comprised of 2 mM uniformly labelled (U-99% 13C; U-99% 15N) protein in 0.03 M cacodylate buffer containing 0.1 M NaCl (pH 6.0) Label: U-99% 13C; U-99% 15N / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 2 mM Component: Molten globule of L94G mutant of horse cytochrome-c Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Ionic strength: 0.03 M cacodylate buffer containing 0.1 M NaCl Not defined Label: 2 mM uniformly labelled (U-99% 13C; U-99% 15N) protein in 0.03 M cacodylate buffer containing 0.1 M NaCl (pH 6.0) pH: 6.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
Software | Name: CNS / Classification: refinement | |||||||||||||||||||||||||||
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NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 7 | |||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | |||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 2000 / Conformers submitted total number: 15 |