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Yorodumi- PDB-1lfp: Crystal Structure of a Conserved Hypothetical Protein Aq1575 from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lfp | ||||||
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Title | Crystal Structure of a Conserved Hypothetical Protein Aq1575 from Aquifex Aeolicus | ||||||
Components | Hypothetical protein AQ_1575Hypothesis | ||||||
Keywords | RNA BINDING PROTEIN / Hypothetical / New fold / thermostability / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å | ||||||
Authors | Shin, D.H. / Yokota, H. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus. Authors: Shin, D.H. / Yokota, H. / Kim, R. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lfp.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lfp.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/1lfp ftp://data.pdbj.org/pub/pdb/validation_reports/lf/1lfp | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28040.400 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O67517 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.63 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 20% PEG3350, 0.2M Ammonium Nitrate, 10 mM NAD, 3% PEG400, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21.5-22.5 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 5.0.2 / Wavelength: 0.97864 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2002 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97864 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→36.2 Å / Num. obs: 22781 / % possible obs: 95.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.9 Å2 |
Reflection shell | Resolution: 1.72→1.73 Å / % possible all: 48 |
Reflection | *PLUS Highest resolution: 1.71 Å / Num. obs: 42899 / % possible obs: 96 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS Highest resolution: 1.71 Å / % possible obs: 48.2 % / Redundancy: 5 % / Num. unique obs: 1081 / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.72→29.88 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 410192.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.9766 Å2 / ksol: 0.297912 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.72→29.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.82 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.71 Å / Lowest resolution: 20 Å / Rfactor obs: 0.228 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.71 Å / Lowest resolution: 1.73 Å / Rfactor obs: 0.215 |