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Yorodumi- PDB-3q6a: X-ray crystal structure of the protein SSP2350 from Staphylococcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q6a | ||||||
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Title | X-ray crystal structure of the protein SSP2350 from Staphylococcus saprophyticus, Northeast structural genomics consortium target SyR116 | ||||||
Components | uncharacterized protein | ||||||
Keywords | Structure Genomics / unknown function / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Staphylococcus saprophyticus | ||||||
Function / homology | Activator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Staphylococcus saprophyticus subsp. saprophyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Seetharaman, J. / Chen, Y. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Seetharaman, J. / Chen, Y. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of the protein SSP2350 from Staphylococcus saprophyticus, Northeast structural genomics consortium target SyR116 Authors: Seetharaman, J. / Chen, Y. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast ...Authors: Seetharaman, J. / Chen, Y. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q6a.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q6a.ent.gz | 187.7 KB | Display | PDB format |
PDBx/mmJSON format | 3q6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q6a_validation.pdf.gz | 477.5 KB | Display | wwPDB validaton report |
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Full document | 3q6a_full_validation.pdf.gz | 497.8 KB | Display | |
Data in XML | 3q6a_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 3q6a_validation.cif.gz | 65.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/3q6a ftp://data.pdbj.org/pub/pdb/validation_reports/q6/3q6a | 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15723.209 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus saprophyticus subsp. saprophyticus (bacteria) Strain: ATCC 15305 / DSM 20229 / Gene: SSP2350 / Production host: Escherichia coli (E. coli) / References: UniProt: Q49US3 #2: 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: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Lithium Chloride 0.1 M, MES 0.1 M, PEG 8000 40%, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 107976 / Num. obs: 107976 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 1.8→1.8 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→43.59 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 132922.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.1207 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→43.59 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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