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Yorodumi- PDB-1nkv: X-RAY STRUCTURE OF YJHP FROM E.COLI NORTHEAST STRUCTURAL GENOMICS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nkv | ||||||
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Title | X-RAY STRUCTURE OF YJHP FROM E.COLI NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER13 | ||||||
Components | HYPOTHETICAL PROTEIN yjhP | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.9 Å | ||||||
Authors | Kuzin, A. / Manor, P. / Benach, J. / Smith, P. / Rost, B. / Xiao, R. / Montelione, G. / Hunt, J. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be published Title: X-RAY STRUCTURE OF YJHP FROM E.COLI NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER13 Authors: Kuzin, A. / Manor, P. / Benach, J. / Smith, P. / Rost, B. / Xiao, R. / Montelione, G. / Hunt, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nkv.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nkv.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 1nkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nkv_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 1nkv_full_validation.pdf.gz | 473.8 KB | Display | |
Data in XML | 1nkv_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 1nkv_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/1nkv ftp://data.pdbj.org/pub/pdb/validation_reports/nk/1nkv | 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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-Components
#1: Protein | Mass: 28782.398 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P39367 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.35 % |
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 18552 / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.1 Å2 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MAD / Resolution: 2.9→19.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 274614.79 / Data cutoff high rms absF: 274614.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: Freidel pairs were used in the refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.225433 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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