+Open data
-Basic information
Entry | Database: PDB / ID: 1iwl | ||||||
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Title | Crystal Structure of the Lipoprotein Localization Factor, LolA | ||||||
Components | Outer-membrane lipoproteins carrier protein | ||||||
Keywords | PROTEIN TRANSPORT / UNCLOSED BETA BARREL | ||||||
Function / homology | Function and homology information lipoprotein localization to outer membrane / lipoprotein transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Takeda, K. / Miyatake, H. / Yokota, N. / Matsuyama, S. / Tokuda, H. / Miki, K. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Crystal structures of bacterial lipoprotein localization factors, LolA and LolB Authors: Takeda, K. / Miyatake, H. / Yokota, N. / Matsuyama, S. / Tokuda, H. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iwl.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iwl.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 1iwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iwl_validation.pdf.gz | 429.3 KB | Display | wwPDB validaton report |
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Full document | 1iwl_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | 1iwl_validation.xml.gz | 11 KB | Display | |
Data in CIF | 1iwl_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/1iwl ftp://data.pdbj.org/pub/pdb/validation_reports/iw/1iwl | 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: 20343.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pYKT102 / Production host: Escherichia coli (E. coli) / References: UniProt: P61316 | ||||
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#2: Chemical | #3: Chemical | #4: 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: 2.39 Å3/Da / Density % sol: 48.07 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG8000, sodium cacodilate, zinc acetate, glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 16, 2001 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. obs: 23909 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.2 % / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.043 |
Reflection shell | Resolution: 1.65→1.71 Å / Num. unique all: 1326 / Rsym value: 0.236 / % possible all: 51.6 |
Reflection | *PLUS Lowest resolution: 40 Å / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 51.6 % / Rmerge(I) obs: 0.236 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.65→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.03
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 1.71 Å |