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Yorodumi- PDB-1lm0: Solution structure and characterization of the heme chaperone CcmE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lm0 | ||||||
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Title | Solution structure and characterization of the heme chaperone CcmE | ||||||
Components | cytochrome c maturation protein E | ||||||
Keywords | CHAPERONE / all-beta protein / heme delivery / cytochrome c maturation / OB-(oligonucleotide binding)fold | ||||||
Function / homology | Function and homology information cytochrome complex assembly / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Shewanella putrefaciens (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dyanamics, restrained energy minimization | ||||||
Authors | Arnesano, F. / Banci, L. / Barker, P.D. / Bertini, I. / Rosato, A. / Su, X.C. / Viezzoli, M.S. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Solution structure and characterization of the heme chaperone CcmE Authors: Arnesano, F. / Banci, L. / Barker, P.D. / Bertini, I. / Rosato, A. / Su, X.C. / Viezzoli, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lm0.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1lm0.ent.gz | 965.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lm0_validation.pdf.gz | 365.9 KB | Display | wwPDB validaton report |
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Full document | 1lm0_full_validation.pdf.gz | 614.7 KB | Display | |
Data in XML | 1lm0_validation.xml.gz | 48.8 KB | Display | |
Data in CIF | 1lm0_validation.cif.gz | 85.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/1lm0 ftp://data.pdbj.org/pub/pdb/validation_reports/lm/1lm0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14714.397 Da / Num. of mol.: 1 / Fragment: water soluble domain of CcmE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella putrefaciens (bacteria) / Gene: ccmE / Plasmid: pPB10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold(DE3) / References: UniProt: O52690, UniProt: Q8EK44*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy on 13C and 15N double labeled apoCcmE. |
-Sample preparation
Details | Contents: 2.0 mM apoCcmE, 20 mM phosphate, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 20 mM phosphate / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dyanamics, restrained energy minimization Software ordinal: 1 Details: 1866 meaningful NOEs and 89 dihedral angle constraints | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: the submitted conformer models are the 35 structures with the lowest target function Conformers calculated total number: 400 / Conformers submitted total number: 35 |