+Open data
-Basic information
Entry | Database: PDB / ID: 3tgo | ||||||
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Title | Crystal structure of the E. coli BamCD complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / lipoprotein complex / TPR repeat / helix-grip fold / Outer membrane protein assembly / outer membrane | ||||||
Function / homology | Function and homology information Bam protein complex / protein insertion into membrane / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / cell surface / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Paetzel, M. / Kim, K.H. / Aulakh, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal structure of the beta-barrel assembly machinery BamCD protein complex Authors: Kim, K.H. / Aulakh, S. / Paetzel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tgo.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tgo.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tgo_validation.pdf.gz | 482.5 KB | Display | wwPDB validaton report |
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Full document | 3tgo_full_validation.pdf.gz | 500.5 KB | Display | |
Data in XML | 3tgo_validation.xml.gz | 33 KB | Display | |
Data in CIF | 3tgo_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/3tgo ftp://data.pdbj.org/pub/pdb/validation_reports/tg/3tgo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 26127.152 Da / Num. of mol.: 2 / Fragment: UNP residues 21-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2595, JW2577, yfiO / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AC02 #2: Protein | Mass: 34711.578 Da / Num. of mol.: 2 / Fragment: UNP residues 26-344 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2477, dapX, JW2462, nlpB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A903 |
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-Non-polymers , 6 types, 132 molecules
#3: Chemical | ChemComp-K / | ||||||||
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#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-NA / | #8: 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: 3.86 Å3/Da / Density % sol: 67.9 % |
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Crystal grow | Temperature: 295 K / pH: 9.2 Details: 0.2 M K2HPO4 and 20% PEG3350, pH 9.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2009 Details: MERIDIONALLY-BENT FUSED SILICA MIRROR WITH PALLADIUM AND UNCOATED STRIPES VERTICALLY- FOCUSING AT 6.6:1 DEMAGNIFICATION |
Radiation | Monochromator: DOUBLE SILICON(111) CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→97.5 Å / Num. obs: 30529 / % possible obs: 99.6 % / Observed criterion σ(I): 5 / Redundancy: 7.2 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 5.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YH6 AND 2YHC Resolution: 2.9→97.45 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.879 / SU B: 12.099 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.758 / ESU R Free: 0.34 / 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: 36.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→97.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.98 Å / Total num. of bins used: 20
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