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Yorodumi- PDB-3ldt: Crystal structure of an Outer membrane protein(OmpA)from Legionel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ldt | ||||||
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Title | Crystal structure of an Outer membrane protein(OmpA)from Legionella pneumophila | ||||||
Components | Outer membrane protein, OmpA family protein | ||||||
Keywords | MEMBRANE PROTEIN / OmpA-like domain / PSI-II / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Satyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of an Outer membrane protein(OmpA)from Legionella pneumophila Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ldt.cif.gz | 40.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ldt.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ldt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/3ldt ftp://data.pdbj.org/pub/pdb/validation_reports/ld/3ldt | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19227.178 Da / Num. of mol.: 1 / Fragment: C-terminal fragment Source method: isolated from a genetically manipulated source Details: TOP 10 (INVITROGEN) / Source: (gene. exp.) Legionella pneumophila (bacteria) Strain: subsp. pneumophila, Philadelphia 1 / ATCC 33152 / DSM 7513) Gene: 3080577, lpg0657 / Plasmid: BC-pSGX3-(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon+RIL / References: UniProt: Q5ZXS4 | ||
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#2: Chemical | #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: 2.77 Å3/Da / Density % sol: 55.66 % |
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Crystal grow | Temperature: 292 K / Method: evaporation / pH: 7 Details: 15% Isopropanol, 1.3M Ammonium Sulpahte , pH 7.0, EVAPORATION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 10001 / Num. obs: 10001 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.5 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.061 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 29.1 % / Mean I/σ(I) obs: 16.8 / Num. unique all: 966 / Rsym value: 0.128 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→40.07 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→40.07 Å
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.038
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