+Open data
-Basic information
Entry | Database: PDB / ID: 4lcn | ||||||
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Title | Crytsal structure of NE0047 in complex with 2'-DEOXY-GUANOSINE | ||||||
Components | Cytidine and deoxycytidylate deaminase zinc-binding region | ||||||
Keywords | HYDROLASE / CDA fold / deaminase | ||||||
Function / homology | Function and homology information guanosine deaminase activity / purine nucleoside catabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Nitrosomonas europaea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Anand, R. / Bitra, A. / Biswas, A. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structural basis of the substrate specificity of cytidine deaminase superfamily Guanine deaminase Authors: Bitra, A. / Biswas, A. / Anand, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lcn.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lcn.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 4lcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lcn_validation.pdf.gz | 768.8 KB | Display | wwPDB validaton report |
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Full document | 4lcn_full_validation.pdf.gz | 774.3 KB | Display | |
Data in XML | 4lcn_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 4lcn_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/4lcn ftp://data.pdbj.org/pub/pdb/validation_reports/lc/4lcn | HTTPS FTP |
-Related structure data
Related structure data | 4lc5C 4lcoC 4lcpC 4ld2C 4ld4C 2g84S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20586.463 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Strain: ATCC 19718 / NBRC 14298 / Gene: NE0047 / Production host: Escherichia coli (E. coli) References: UniProt: Q82Y41, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds #2: Chemical | #3: Chemical | ChemComp-GNG / | #4: Chemical | #5: 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: 1.85 Å3/Da / Density % sol: 33.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.225M MgCl2, 25% PEG 3350, 0.1M Bis-Tris (pH 5.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→35.92 Å / Num. all: 23864 / Num. obs: 23864 / % possible obs: 81.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 4 / % possible all: 79.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G84 Resolution: 1.8→34.76 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.596 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.385 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→34.76 Å
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Refine LS restraints |
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