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Yorodumi- PDB-1nh9: Crystal Structure of a DNA Binding Protein Mja10b from the hypert... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nh9 | ||||||
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Title | Crystal Structure of a DNA Binding Protein Mja10b from the hyperthermophile Methanococcus jannaschii | ||||||
Components | DNA-binding protein Alba | ||||||
Keywords | DNA BINDING PROTEIN / Mja10b | ||||||
Function / homology | Function and homology information chromosome condensation / chromosome / double-stranded DNA binding / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wang, G. / Bartlam, M. / Guo, R. / Yang, H. / Xue, H. / Liu, Y. / Huang, L. / Rao, Z. | ||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: Crystal structure of a DNA binding protein from the hyperthermophilic euryarchaeon Methanococcus jannaschii Authors: Wang, G. / Guo, R. / Bartlam, M. / Yang, H. / Xue, H. / Liu, Y. / Huang, L. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nh9.cif.gz | 27 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nh9.ent.gz | 17.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nh9_validation.pdf.gz | 401.7 KB | Display | wwPDB validaton report |
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Full document | 1nh9_full_validation.pdf.gz | 402.7 KB | Display | |
Data in XML | 1nh9_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 1nh9_validation.cif.gz | 4.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/1nh9 ftp://data.pdbj.org/pub/pdb/validation_reports/nh/1nh9 | HTTPS FTP |
-Related structure data
Related structure data | 1h0xS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer in the asymmetric unit |
-Components
#1: Protein | Mass: 9690.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57665 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.69 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.25 Details: Tris-HCl, MPD, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Wang, G.G., (2002) Acta Cryst., D58, 1240. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9868 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Apr 15, 2002 / Details: mirrors |
Radiation | Monochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9868 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 7093 / Num. obs: 7093 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 4.2 / Num. unique all: 692 / % possible all: 99.1 |
Reflection | *PLUS Num. obs: 6946 / % possible obs: 96.6 % / Redundancy: 13.1 % / Num. measured all: 91002 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.06 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 6.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1h0x Resolution: 2→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.06 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 12
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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