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Yorodumi- PDB-4pag: ABC transporter solute binding protein from Sulfurospirillum dele... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pag | ||||||
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Title | ABC transporter solute binding protein from Sulfurospirillum deleyianum DSM 6946 | ||||||
Components | Periplasmic binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / ABC transporter / solute binding protein | ||||||
Function / homology | Function and homology information Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2180 / : / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2180 / : / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Sulfurospirillum deleyianum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å | ||||||
Authors | Chang, C. / Endres, M. / Li, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of ABC transporter solute binding protein from Sulfurospirillum deleyianum DSM 6946 Authors: Chang, C. / Endres, M. / Li, H. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pag.cif.gz | 302.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pag.ent.gz | 245.3 KB | Display | PDB format |
PDBx/mmJSON format | 4pag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pag_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 4pag_full_validation.pdf.gz | 465.5 KB | Display | |
Data in XML | 4pag_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 4pag_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/4pag ftp://data.pdbj.org/pub/pdb/validation_reports/pa/4pag | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37388.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfurospirillum deleyianum (bacteria) / Strain: ATCC 51133 / DSM 6946 / 5175 / Gene: Sdel_2069 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1B4R1 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-HIS / | #5: 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: 2.56 Å3/Da / Density % sol: 51.98 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: magnesiun chloride, MES, PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double crystal / 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→50 Å / Num. all: 59912 / Num. obs: 59880 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.119 / Χ2: 0.799 / Net I/av σ(I): 16.769 / Net I/σ(I): 6.8 / Num. measured all: 426232 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.901→40.21 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.321 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.425 / ESU R Free: 0.128 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 80.34 Å2 / Biso mean: 24.137 Å2 / Biso min: 10.48 Å2
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Refinement step | Cycle: final / Resolution: 1.901→40.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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