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Yorodumi- PDB-2oys: Crystal Structure of SP1951 protein from Streptococcus pneumoniae... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oys | ||||||
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Title | Crystal Structure of SP1951 protein from Streptococcus pneumoniae in complex with FMN, Northeast Structural Genomics Target SpR27 | ||||||
Components | Hypothetical protein SP1951 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Forouhar, F. / Lee, I. / Vorobiev, S.M. / Janjua, H. / Satterwhite, R. / Liu, J. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Forouhar, F. / Lee, I. / Vorobiev, S.M. / Janjua, H. / Satterwhite, R. / Liu, J. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2007 Title: Functional insights from structural genomics. Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / ...Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / Pichersky, E. / Klessig, D.F. / Porter, C.W. / Montelione, G.T. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oys.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oys.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 2oys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oys_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2oys_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2oys_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 2oys_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/2oys ftp://data.pdbj.org/pub/pdb/validation_reports/oy/2oys | HTTPS FTP |
-Related structure data
Related structure data | 1rtyC 1sqsSC 1tm0C 1zbpC 2hd3C 2nv4C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28439.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1951 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q97NR6, UniProt: A0A0H2URW2*PLUS #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: 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: 2.15 Å3/Da / Density % sol: 42.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10 mM Tris-HCl pH 7.5, 20% PEG 8000, 50 mM NaCl, 5 mM DTT, 10 mM FMN, 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: Jul 24, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.75 Å / Num. all: 33663 / Num. obs: 33663 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 6.6 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.089 / Net I/σ(I): 24.77 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 12.23 / Rsym value: 0.301 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SQS Resolution: 2→29.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 314751.75 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.554 Å2 / ksol: 0.328039 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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