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Yorodumi- PDB-1n4d: The Ligand-Free Structure of E coli BtuF, the Periplasmic Binding... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n4d | ||||||
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Title | The Ligand-Free Structure of E coli BtuF, the Periplasmic Binding Protein for Vitamin B12 | ||||||
Components | Vitamin B12 transport protein btuF | ||||||
Keywords | TRANSPORT PROTEIN / ABC transporter / Vitamin B12 / periplasmic binding protein / transmembrane transport | ||||||
Function / homology | Function and homology information cobalamin transport complex / cobalamin transport / cobalamin binding / outer membrane-bounded periplasmic space / periplasmic space / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Karpowich, N. / Smith, P.C. / Hunt, J.F. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2003 Title: Crystal Structures of the BtuF Periplasmic-binding Protein for Vitamin B12 Suggest a Functionally Important Reduction in Protein Mobility upon Ligand Binding Authors: Karpowich, N.K. / Huang, H.H. / Smith, P.C. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n4d.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n4d.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 1n4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/1n4d ftp://data.pdbj.org/pub/pdb/validation_reports/n4/1n4d | HTTPS FTP |
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-Related 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: 28140.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET24A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bL21(DE3) / References: UniProt: P37028 |
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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: 2.41 Å3/Da / Density % sol: 48.62 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: acetate, PEG4000, (NH4)OAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Oct 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 12293 / Biso Wilson estimate: 56.6 Å2 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 83.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Rfactor Rfree error: 0.027 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 63.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.14 Å / Rfactor Rfree error: 0.069 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.236 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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