+Open data
-Basic information
Entry | Database: PDB / ID: 2een | ||||||
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Title | Structure of PH1819 protein from Pyrococcus Horikoshii OT3 | ||||||
Components | Hypothetical protein PH1819 | ||||||
Keywords | Structural Genomics / Unknown Function / Dimer / Hypothetical Protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Adenylyl cyclase CyaB / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Bagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of PH1819 protein from Pyrococcus Horikoshii OT3 Authors: Bagautdinov, B. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2een.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2een.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 2een.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2een_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 2een_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 2een_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 2een_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/2een ftp://data.pdbj.org/pub/pdb/validation_reports/ee/2een | HTTPS FTP |
-Related structure data
Related structure data | 2dc4S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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 dimer. |
-Components
#1: Protein | Mass: 22131.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1819 / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O59483 #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: 2.1 Å3/Da / Density % sol: 41.32 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 8.4 Details: 27.5w/w(%) PEG 4000, 0.1M TRIS-HCL, pH 8.4, microbatch, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 22, 2006 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→33.18 Å / Num. all: 45107 / Num. obs: 44006 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.045 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4418 / Rsym value: 0.332 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DC4 Resolution: 1.65→33.18 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→33.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.71 Å / Rfactor Rfree error: 0.022
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