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Yorodumi- PDB-2r88: Crystal structure of the long-chain fatty acid transporter FadL m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r88 | ||||||
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Title | Crystal structure of the long-chain fatty acid transporter FadL mutant delta S3 kink | ||||||
Components | Long-chain fatty acid transport protein | ||||||
Keywords | TRANSPORT PROTEIN / beta barrel / outer membrane protein / Lipid transport / Phage recognition / Transmembrane / Transport | ||||||
Function / homology | Function and homology information long-chain fatty acid transporting porin activity / ligand-gated channel activity / cell outer membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Hearn, E.M. / Patel, D.R. / Lepore, B.W. / Indic, M. / van den Berg, B. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Transmembrane passage of hydrophobic compounds through a protein channel wall Authors: Hearn, E.M. / Patel, D.R. / Lepore, B.W. / Indic, M. / van den Berg, B. #1: Journal: Science / Year: 2004 Title: Crystal structure of the long-chain fatty acid transporter FadL Authors: van den Berg, B. / Black, P.N. / Clemons Jr., W.M. / Rapoport, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r88.cif.gz | 148.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r88.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 2r88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/2r88 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/2r88 | HTTPS FTP |
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-Related structure data
Related structure data | 2r4lC 2r4nC 2r4oC 2r4pC 3dwnC 3dwoC 1t16S 2r4m S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
#1: Protein | Mass: 46633.801 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fadL, ttr / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P10384 Sequence details | SEQUENCE RESIDUES S100, N101, Y102, AND G103 WERE REPLACED WITH RESIDUES ALA, ASN, AND ASP TO FORM ...SEQUENCE RESIDUES S100, N101, Y102, AND G103 WERE REPLACED WITH RESIDUES ALA, ASN, AND ASP TO FORM THE DELTA S3 KINK. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 5000 MME, 0.2M ammonium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 2007 |
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→31.9 Å / Num. obs: 33965 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.3 / Redundancy: 8.9 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3041 / Rsym value: 0.563 / % possible all: 84.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T16 Resolution: 2.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 49.67 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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