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Yorodumi- PDB-2gsl: X-Ray Crystal Structure of Protein FN1578 from Fusobacterium nucl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gsl | ||||||
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Title | X-Ray Crystal Structure of Protein FN1578 from Fusobacterium nucleatum. Northeast Structural Genomics Consortium Target NR1. | ||||||
Components | Hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-helical protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Fusobacterium nucleatum subsp. nucleatum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Forouhar, F. / Su, M. / Jayaraman, S. / Conover, K. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Hypothetical Protein (FN1578) from Fusobacterium nucleatum, NESG Target NR1 Authors: Forouhar, F. / Su, M. / Jayaraman, S. / Conover, K. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gsl.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gsl.ent.gz | 133.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gsl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gsl_validation.pdf.gz | 478.3 KB | Display | wwPDB validaton report |
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Full document | 2gsl_full_validation.pdf.gz | 503 KB | Display | |
Data in XML | 2gsl_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 2gsl_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/2gsl ftp://data.pdbj.org/pub/pdb/validation_reports/gs/2gsl | 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: 16261.394 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (bacteria) Species: Fusobacterium nucleatum / Strain: ATCC 25586 / Gene: FN1578 / Plasmid: pETXL-10 Gold / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: GenBank: 19712792, UniProt: Q8RIL0*PLUS #2: Chemical | ChemComp-MG / #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: 2.61 Å3/Da / Density % sol: 52.81 % |
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Crystal grow | Temperature: 293 K / pH: 7 Details: 100mM HEPES, 100mM Mg(NO3)2, 20% PEG8K, 5 mM DTT, Microbatch under oil, pH 7, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2006 / Details: Mirrors. |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29.45 Å / Num. all: 60679 / Num. obs: 60619 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.081 / Net I/σ(I): 13.31 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3 / Num. unique all: 6068 / Rsym value: 0.509 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→29.45 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 162894.17 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.2765 Å2 / ksol: 0.328052 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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