[English] 日本語
Yorodumi- PDB-2b1l: Crystal structure of N-terminal 57 residue deletion mutant of E. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b1l | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of N-terminal 57 residue deletion mutant of E. coli CcmG protein(residues 58-185) | ||||||
Components | Thiol:disulfide interchange protein dsbE | ||||||
Keywords | OXIDOREDUCTASE / Comparison with the E.coli CcmG / folding topology change | ||||||
Function / homology | Function and homology information cytochrome complex assembly / disulfide oxidoreductase activity / outer membrane-bounded periplasmic space / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ouyang, N. / Gao, Y.G. / Hu, H.Y. / Xia, Z.X. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Crystal structures of E. coli CcmG and its mutants reveal key roles of the N-terminal beta-sheet and the fingerprint region Authors: Ouyang, N. / Gao, Y.G. / Hu, H.Y. / Xia, Z.X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2b1l.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2b1l.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 2b1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/2b1l ftp://data.pdbj.org/pub/pdb/validation_reports/b1/2b1l | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14720.697 Da / Num. of mol.: 2 / Mutation: N-terminal 57 residue deletion mutant Source method: isolated from a genetically manipulated source Details: N-terminal 57 residue deletion mutant / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ccmg / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA86 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 41.56 % |
---|---|
Crystal grow | Temperature: 293 K / Method: seeding / pH: 7.8 Details: HEPES buffer, ammonium sulfate, PEG 4000, pH 7.8, Seeding, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 20230 / Num. obs: 19846 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.053 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.233 / Num. unique all: 1722 / % possible all: 85.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: structure of E.coli CcmG Resolution: 1.9→29.14 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 285770.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.0236 Å2 / ksol: 0.309022 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|