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Yorodumi- PDB-1fux: CRYSTAL STRUCTURE OF E.COLI YBCL, A NEW MEMBER OF THE MAMMALIAN P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fux | ||||||
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Title | CRYSTAL STRUCTURE OF E.COLI YBCL, A NEW MEMBER OF THE MAMMALIAN PEBP FAMILY | ||||||
Components | HYPOTHETICAL 19.5 KDA PROTEIN IN EMRE-RUS INTERGENIC REGION | ||||||
Keywords | UNKNOWN FUNCTION / BETA PROTEIN | ||||||
Function / homology | Function and homology information negative regulation of catalytic activity / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Serre, L. / Pereira de Jesus, K. / Benedetti, H. / Bureaud, N. / Schoentgen, F. / Zelwer, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fux.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fux.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/1fux ftp://data.pdbj.org/pub/pdb/validation_reports/fu/1fux | HTTPS FTP |
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-Related structure data
Related structure data | 1fjjSC 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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Unit cell |
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Details | the biological assembly is a dimer constructed from chain A and chain B |
-Components
#1: Protein | Mass: 17816.643 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PERIPLASMIC FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PIN-III-OMPA2 / Production host: Escherichia coli (E. coli) / Keywords: PERIPLASMIC FORM / References: UniProt: P77368 #2: Water | ChemComp-HOH / | Nonpolymer details | MOLECULES 401, 402, 403, 404 HAVE BEEN MODELED BY HOH BUT CORRESPOND TO UNKNOWN MOLECULES PRESENT ...MOLECULES 401, 402, 403, 404 HAVE BEEN MODELED BY HOH BUT CORRESPOND | |
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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: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: PEG 6000, Hepes, pH 7.3, 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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97941 |
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: 0.97941 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→25 Å / Num. obs: 96044 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 16.894 Å2 / Rsym value: 0.03 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.81→1.91 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 3751 / Rsym value: 0.088 / % possible all: 89.4 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 28148 / Num. measured all: 96044 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS Rmerge(I) obs: 0.088 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FJJ E.COLI YBHB Resolution: 1.81→25 Å / SU B: 3.31573 / SU ML: 0.10434 / Cross valid method: FREE-R / σ(F): 0 / σ(I): 0 / ESU R: 0.16318 / ESU R Free: 0.15721 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 21.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→25 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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