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- PDB-1fjj: CRYSTAL STRUCTURE OF E.COLI YBHB PROTEIN, A NEW MEMBER OF THE MAM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fjj | ||||||
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Title | CRYSTAL STRUCTURE OF E.COLI YBHB PROTEIN, A NEW MEMBER OF THE MAMMALIAN PEBP FAMILY | ||||||
![]() | HYPOTHETICAL 17.1 KDA PROTEIN IN MODC-BIOA INTERGENIC REGION | ||||||
![]() | LIPID BINDING PROTEIN / PEPB family | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Serre, L. / Pereira de Jesus, K. / Benedetti, H. / Bureaud, N. / Schoentgen, F. / Zelwer, C. | ||||||
![]() | ![]() Title: Crystal structures of YBHB and YBCL from Escherichia coli, two bacterial homologues to a Raf kinase inhibitor protein. Authors: Serre, L. / Pereira de Jesus, K. / Zelwer, C. / Bureaud, N. / Schoentgen, F. / Benedetti, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.3 KB | Display | ![]() |
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PDB format | ![]() | 34.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 369.2 KB | Display | ![]() |
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Full document | ![]() | 369.6 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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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Details | the biological assembly is a dimer constructed from chain A and a symmetry partner generated by a crystallography two-fold (the dimer has been suggested by gel filtration results) |
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Components
#1: Protein | Mass: 17409.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-EPE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Sodium citrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→25 Å / Num. all: 165834 / Num. obs: 165834 / % possible obs: 96.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.045 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.66→1.75 Å / Redundancy: 4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4024 / Rsym value: 0.44 / % possible all: 76.3 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 35266 / Num. measured all: 165834 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS Rmerge(I) obs: 0.44 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 22.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→25 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |