+Open data
-Basic information
Entry | Database: PDB / ID: 4frt | ||||||
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Title | Crystal Structure of Pseudomonas aeruginosa OccK7 (OpdD) | ||||||
Components | Probable porin | ||||||
Keywords | TRANSPORT PROTEIN / Beta-barrel / transporter (porin) / outer membrane | ||||||
Function / homology | Outer membrane porin, bacterial / outer membrane porin, OprD family / Porin domain superfamily / channel activity / porin activity / membrane => GO:0016020 / Probable porin Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.166 Å | ||||||
Authors | Eren, E. / van den Berg, B. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of OccK Subfamily Proteins Authors: Eren, E. / van den Berg, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4frt.cif.gz | 305 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4frt.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4frt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/4frt ftp://data.pdbj.org/pub/pdb/validation_reports/fr/4frt | HTTPS FTP |
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-Related structure data
Related structure data | 4frxC 4fsoC 4fspC 4ft6C 3t24S 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: 45169.043 Da / Num. of mol.: 2 / Fragment: unp residues 23-416 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA1025 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4U9 #2: Water | ChemComp-HOH / | |
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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: 3.91 Å3/Da / Density % sol: 68.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 400, 1M sodium formate, 0.05M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9764 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 1, 2012 |
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9764 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→40 Å / Num. obs: 23348 / % possible obs: 99.1 % / Redundancy: 7.7 % / Rsym value: 0.136 / Net I/σ(I): 18 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.55 / Rsym value: 0.889 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3T24 Resolution: 3.166→14.989 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 29.55 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.166→14.989 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: 29.5551 Å / Origin y: 3.8155 Å / Origin z: 24.2818 Å
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Refinement TLS group | Selection details: all |