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Yorodumi- PDB-4lmi: Crystal structure of putative ketosteroid isomerase from Kribbell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lmi | ||||||
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Title | Crystal structure of putative ketosteroid isomerase from Kribbella flavida DSM 17836 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | Structural genomics / unknown function / PSI-BIOLOGY / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SnoaL-like domain-containing protein Function and homology information | ||||||
Biological species | Kribbella flavida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Chang, C. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of putative ketosteroid isomerase from Kribbella flavida DSM 17836 Authors: Chang, C. / Chhor, G. / Endres, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lmi.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lmi.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/4lmi ftp://data.pdbj.org/pub/pdb/validation_reports/lm/4lmi | 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: 15767.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_6894 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D2Q2I7 #2: Chemical | #3: 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: 2.55 Å3/Da / Density % sol: 51.75 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M di-Ammonium hydrogen Citrate, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2012 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 30818 / Num. obs: 30387 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.98 / Num. unique all: 1453 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.168 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.114 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.15 Å2 / Biso mean: 34.2618 Å2 / Biso min: 16.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.795→1.842 Å / Total num. of bins used: 20
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