+Open data
-Basic information
Entry | Database: PDB / ID: 2e9y | ||||||
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Title | Crystal structure of project APE1968 from Aeropyrum pernix K1 | ||||||
Components | Carbamate kinase | ||||||
Keywords | TRANSFERASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Shimizu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of project APE1968 from Aeropyrum pernix K1 Authors: Shimizu, K. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e9y.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e9y.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 2e9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e9y_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 2e9y_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | 2e9y_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 2e9y_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/2e9y ftp://data.pdbj.org/pub/pdb/validation_reports/e9/2e9y | HTTPS FTP |
-Related structure data
Related structure data | 1e19S 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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-Components
#1: Protein | Mass: 33707.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pET 21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 CodonPlus (DE3)-RIL / References: UniProt: Q9YAH1, carbamate kinase #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: 2.32 Å3/Da / Density % sol: 47.08 % |
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Crystal grow | Temperature: 291 K / Method: microbach / pH: 5.65 Details: 16.5% (w/v) PEG 20K, 0.1M Citr., pH 5.65, Microbach, temperature 291K |
-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: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 19, 2006 / Details: Mirror |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 58985 / Num. obs: 58985 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 22.102 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.065 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.317 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1E19 Resolution: 1.8→37.48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2070175.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.9369 Å2 / ksol: 0.330158 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→37.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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