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Yorodumi- PDB-3uif: CRYSTAL STRUCTURE OF putative sulfonate ABC transporter, periplas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uif | ||||||
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Title | CRYSTAL STRUCTURE OF putative sulfonate ABC transporter, periplasmic sulfonate-binding protein SsuA from Methylobacillus flagellatus KT | ||||||
Components | Sulfonate ABC transporter, periplasmic sulfonate-binding protein SsuA | ||||||
Keywords | TRANSPORT PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGRC / sulfonate ABC transporter / PSI-Biology / New York Structural Genomics Research Consortium | ||||||
Function / homology | SsuA/THI5-like / NMT1/THI5 like / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Sulfonate ABC transporter, periplasmic sulfonate-binding protein SsuA Function and homology information | ||||||
Biological species | Methylobacillus flagellatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Malashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: CRYSTAL STRUCTURE OF putative sulfonate ABC transporter, periplasmic sulfonate-binding protein SsuA from Methylobacillus flagellatus KT Authors: Malashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Seidel, R. / 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 | 3uif.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uif.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 3uif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uif_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
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Full document | 3uif_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 3uif_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 3uif_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/3uif ftp://data.pdbj.org/pub/pdb/validation_reports/ui/3uif | 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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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 39219.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacillus flagellatus (bacteria) / Strain: KT / Gene: 4000324, Mfla_1563 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q1H106 | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.18 Å3/Da / Density % sol: 43.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Li-sulfate, 0.1 M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 22865 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.11 / Χ2: 1.18 / Net I/σ(I): 7.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→19.78 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.1717 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8081 / SU B: 24.775 / SU ML: 0.254 / SU R Cruickshank DPI: 0.2609 / SU Rfree: 0.3719 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
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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: 85.57 Å2 / Biso mean: 49.1495 Å2 / Biso min: 35.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 1.8947 Å / Origin y: 26.8726 Å / Origin z: 3.8492 Å
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