+Open data
-Basic information
Entry | Database: PDB / ID: 2yhc | ||||||
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Title | Structure of BamD from E. coli | ||||||
Components | UPF0169 LIPOPROTEIN YFIO | ||||||
Keywords | MEMBRANE PROTEIN / LIPOPROTEIN / ESSENTIAL BAM COMPONENT | ||||||
Function / homology | Function and homology information Bam protein complex / protein insertion into membrane / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.8 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 | 2yhc.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yhc.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 2yhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yhc_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
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Full document | 2yhc_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | 2yhc_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 2yhc_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/2yhc ftp://data.pdbj.org/pub/pdb/validation_reports/yh/2yhc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25959.949 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AC02 |
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#2: Chemical | ChemComp-URE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.14 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 30% PEG 4000, 10% I-PROH, 0.1 M HEPES PH 7.5 . |
-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: 1.8→40 Å / Num. obs: 16896 / % possible obs: 99.4 % / Observed criterion σ(I): 3.9 / Redundancy: 6.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.9 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 1.8→28.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.041 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.139 / 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: 44.667 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→28.39 Å
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Refine LS restraints |
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