+Open data
-Basic information
Entry | Database: PDB / ID: 3q5m | ||||||
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Title | Crystal structure of Escherichia coli BamD | ||||||
Components | UPF0169 lipoprotein yfiO | ||||||
Keywords | PROTEIN BINDING / Lipoprotein / BamD | ||||||
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 Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.604 Å | ||||||
Authors | Dong, C. / Hou, H. / Yang, X. / Dong, Y. / Shen, Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structure of Escherichia coli BamD and its functional implications in outer membrane protein assembly Authors: Dong, C. / Hou, H.F. / Yang, X. / Shen, Y.Q. / Dong, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q5m.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q5m.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 3q5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/3q5m ftp://data.pdbj.org/pub/pdb/validation_reports/q5/3q5m | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25640.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yfiO / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC02 | ||
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#2: Chemical | ChemComp-IOD / #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: 3.6 Å3/Da / Density % sol: 65.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.14M KI, 26%-27% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9791 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 11964 / Num. obs: 10307 / % possible obs: 86.2 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2 / Redundancy: 23.3 % / Rmerge(I) obs: 0.107 / Rsym value: 0.133 / Net I/σ(I): 41.38 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1155 / Rsym value: 0.643 / % possible all: 99.9 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD / Resolution: 2.604→32.602 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 2.49 / σ(I): 2 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.06 Å2 / ksol: 0.333 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.604→32.602 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 37.665 Å / Origin y: -0.7724 Å / Origin z: 36.543 Å
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Refinement TLS group | Selection details: all |