+Open data
-Basic information
Entry | Database: PDB / ID: 1nps | ||||||
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Title | CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF PROTEIN S | ||||||
Components | DEVELOPMENT-SPECIFIC PROTEIN S | ||||||
Keywords | SIGNALING PROTEIN / CRYSTALLINE LIKE STRUCTURE | ||||||
Function / homology | Function and homology information structural constituent of eye lens / sporulation resulting in formation of a cellular spore / metal ion binding Similarity search - Function | ||||||
Biological species | Myxococcus xanthus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wenk, M. / Baumgartner, R. / Mayer, E.M. / Huber, R. / Holak, T.A. / Jaenicke, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The domains of protein S from Myxococcus xanthus: structure, stability and interactions. Authors: Wenk, M. / Baumgartner, R. / Holak, T.A. / Huber, R. / Jaenicke, R. / Mayr, E.M. #1: Journal: Structure / Year: 1994 Title: NMR-Derived Three-Dimensional Solution Structure of Protein S Complexed with Calcium Authors: Bagby, S. / Harvey, T.S. / Eagle, S.G. / Inouye, S. / Ikura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nps.cif.gz | 30.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nps.ent.gz | 19.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nps_validation.pdf.gz | 360.3 KB | Display | wwPDB validaton report |
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Full document | 1nps_full_validation.pdf.gz | 361.1 KB | Display | |
Data in XML | 1nps_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 1nps_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1nps ftp://data.pdbj.org/pub/pdb/validation_reports/np/1nps | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9389.440 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN: MOTIFS 1-2 AND LINKER Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (bacteria) / Cellular location: CYTOSOL / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02966 | ||
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#2: Chemical | #3: 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: 2.05 Å3/Da / Density % sol: 40.05 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 36 % | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 7.5 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 1, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 7166 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.198 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.9 |