+Open data
-Basic information
Entry | Database: PDB / ID: 2rc3 | ||||||
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Title | Crystal structure of CBS domain, NE2398 | ||||||
Components | CBS domain | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / CBS domain / in situ proteolysis / Br / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nitrosomonas europaea ATCC 19718 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Dong, A. / Xu, X. / Korniyenko, Y. / Yakunin, A. / Zheng, H. / Walker, J.R. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of CBS domain, NE2398. Authors: Dong, A. / Xu, X. / Korniyenko, A. / Yakunin, A. / Zheng, H. / Walker, J.R. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rc3.cif.gz | 130.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rc3.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 2rc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/2rc3 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/2rc3 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
-Components
#1: Protein | Mass: 15169.631 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria) Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: NE2398 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q82SE2 #2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-NAD / #4: 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: 2.09 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 0.1M Na(OAC) pH 5.2, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9197 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 11, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9197 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 67993 / Num. obs: 67993 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.57 / Num. unique all: 6501 / Rsym value: 0.682 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.923 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs COOT 1.0, ARP/wARP 6.1.1 have also been used in refinement
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.641 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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