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Yorodumi- PDB-3q7m: The crystal structure of BamB from the BAM complex in spacegroup I222 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q7m | ||||||
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Title | The crystal structure of BamB from the BAM complex in spacegroup I222 | ||||||
Components | Lipoprotein yfgL | ||||||
Keywords | PROTEIN BINDING / beta-propeller / BAM complex / outer membrane protein folding / Gram negative / BamA | ||||||
Function / homology | Function and homology information Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.651 Å | ||||||
Authors | Noinaj, N. / Fairman, J.W. / Buchanan, S.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: The Crystal Structure of BamB Suggests Interactions with BamA and Its Role within the BAM Complex. Authors: Noinaj, N. / Fairman, J.W. / Buchanan, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q7m.cif.gz | 143.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q7m.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 3q7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/3q7m ftp://data.pdbj.org/pub/pdb/validation_reports/q7/3q7m | HTTPS FTP |
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-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: 40423.871 Da / Num. of mol.: 1 / Fragment: UNP residues 21-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yfgL, b2512, JW2496 / Production host: Escherichia coli (E. coli) / References: UniProt: P77774 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.18 M triammonium citrate, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 / Wavelength: 0.97944, 0.97960, 0.94944 | |||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 8, 2010 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.65→50 Å / Num. all: 48256 / Num. obs: 48256 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rsym value: 0.08 / Net I/σ(I): 24.1 | |||||||||||||||
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.88 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.651→19.378 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 19.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.114 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.651→19.378 Å
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Refine LS restraints |
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LS refinement shell |
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