+Open data
-Basic information
Entry | Database: PDB / ID: 4ld4 | ||||||
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Title | Crystal structure of NE0047 in complex with cytosine | ||||||
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: 3 Å | ||||||
Authors | Bitra, A. / Biswas, A. / Anand, R. | ||||||
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 | 4ld4.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ld4.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ld4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ld4_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
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Full document | 4ld4_full_validation.pdf.gz | 464.7 KB | Display | |
Data in XML | 4ld4_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 4ld4_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/4ld4 ftp://data.pdbj.org/pub/pdb/validation_reports/ld/4ld4 | HTTPS FTP |
-Related structure data
Related structure data | 4lc5C 4lcnC 4lcoC 4lcpC 4ld2C 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-CYT / | #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: 1.9 Å3/Da / Density % sol: 35.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.225M MgCl2, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 |
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Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→55.18 Å / Num. all: 6717 / Num. obs: 6717 / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 7.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G84 Resolution: 3→50 Å / Occupancy max: 1 / Occupancy min: 0.3 / σ(F): 0
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Solvent computation | Bsol: 21.8885 Å2 | ||||||||||||||||||||
Displacement parameters | Biso max: 79.97 Å2 / Biso mean: 16.8344 Å2 / Biso min: 1 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.08 Å / Total num. of bins used: 20
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Xplor file |
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