+Open data
-Basic information
Entry | Database: PDB / ID: 2db0 | ||||||
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Title | Crystal structure of PH0542 | ||||||
Components | 253aa long hypothetical protein | ||||||
Keywords | PROTEIN BINDING / HEAT repeats / helical structure / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Repeat of uncharacterized protein PH0542 / Repeat of uncharacterized protein PH0542 / HEAT repeat / HEAT repeat / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe ...Repeat of uncharacterized protein PH0542 / Repeat of uncharacterized protein PH0542 / HEAT repeat / HEAT repeat / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Nishino, A. / Handa, N. / Kishishita, S. / Murayama, K. / Shirouzu, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of PH0542 Authors: Handa, N. / Nishino, A. / Kishishita, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2db0.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2db0.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 2db0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2db0_validation.pdf.gz | 436.1 KB | Display | wwPDB validaton report |
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Full document | 2db0_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 2db0_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 2db0_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/2db0 ftp://data.pdbj.org/pub/pdb/validation_reports/db/2db0 | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28734.666 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pRARE / References: UniProt: O58277 #2: 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: 2.07 Å3/Da / Density % sol: 40.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG3350, 0.2M ammonium acetate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9790, 0.9797, 0.9670 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 20, 2005 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→50 Å / Num. obs: 24884 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rsym value: 0.075 / Net I/σ(I): 17 | ||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 4.6 / Rsym value: 0.369 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: This structure was refined also by CNS 1.1.
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Displacement parameters | Biso mean: 36.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å
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