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Yorodumi- PDB-3l6u: Crystal structure of abc-type sugar transport system, Periplasmic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l6u | ||||||
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Title | Crystal structure of abc-type sugar transport system, Periplasmic component from exiguobacterium sibiricum | ||||||
Components | ABC-TYPE SUGAR TRANSPORT SYSTEM PERIPLASMIC COMPONENT | ||||||
Keywords | TRANSPORT PROTEIN / structural genomics / NYSGRC / target 11006s / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / membrane => GO:0016020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Periplasmic binding protein/LacI transcriptional regulator Function and homology information | ||||||
Biological species | Exiguobacterium sibiricum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of abc-type sugar transport system, Periplasmic component from exiguobacterium sibiricum Authors: Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l6u.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l6u.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 3l6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l6u_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 3l6u_full_validation.pdf.gz | 467.6 KB | Display | |
Data in XML | 3l6u_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 3l6u_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/3l6u ftp://data.pdbj.org/pub/pdb/validation_reports/l6/3l6u | HTTPS FTP |
-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: 33102.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Exiguobacterium sibiricum (bacteria) / Strain: DSM 17290 / JCM 13490 / 255-15 / Gene: Exig_0838 / Production host: Escherichia coli (E. coli) / References: UniProt: B1YL86 #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: 2.03 Å3/Da / Density % sol: 39.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 3350, 0.1 Bis-Tris, 0.1M Lithium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 25, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 41731 / Num. obs: 41731 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.063 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→24.85 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1191803.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.8799 Å2 / ksol: 0.417296 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.85 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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Xplor file |
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