+Open data
-Basic information
Entry | Database: PDB / ID: 2yh6 | ||||||
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Title | Structure of the N-terminal domain of BamC from E. coli | ||||||
Components | LIPOPROTEIN 34 | ||||||
Keywords | LIPID BINDING PROTEIN | ||||||
Function / homology | Function and homology information Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell surface / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.55 Å | ||||||
Authors | Zeth, K. / Albrecht, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural Basis of Outer Membrane Protein Biogenesis in Bacteria. Authors: Albrecht, R. / Zeth, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yh6.cif.gz | 184 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yh6.ent.gz | 155 KB | Display | PDB format |
PDBx/mmJSON format | 2yh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/2yh6 ftp://data.pdbj.org/pub/pdb/validation_reports/yh/2yh6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 12532.893 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 101-212 Source method: isolated from a genetically manipulated source Details: DOMAIN WAS IDENTIFIED BY LIMITED PROTEOLYSIS / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A903 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | THE DOMAIN WAS IDENTIFIED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.24 % / Description: NONE |
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Crystal grow | pH: 3.5 / Details: 2 M (NH4)2SO4, 0.1 M CITRIC ACID PH 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. obs: 56570 / % possible obs: 95.1 % / Observed criterion σ(I): 2.7 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.55→1.59 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / % possible all: 93.8 |
-Processing
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.907 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.031 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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