+Open data
-Basic information
Entry | Database: PDB / ID: 3bzg | ||||||
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Title | UVDE pH4.4 | ||||||
Components | UV endonuclease | ||||||
Keywords | HYDROLASE / TIM barrel / UVDE / DNA repair / endonuclease | ||||||
Function / homology | Function and homology information response to UV / nucleotide-excision repair / endonuclease activity / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Meulenbroek, E.M. / Paspaleva, K. / Thomassen, E.A.J. / Abrahams, J.P. / Goosen, N. / Pannu, N.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Involvement of a carboxylated lysine in UV damage endonuclease Authors: Meulenbroek, E.M. / Paspaleva, K. / Thomassen, E.A. / Abrahams, J.P. / Goosen, N. / Pannu, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bzg.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bzg.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 3bzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bzg_validation.pdf.gz | 427.3 KB | Display | wwPDB validaton report |
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Full document | 3bzg_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 3bzg_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 3bzg_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/3bzg ftp://data.pdbj.org/pub/pdb/validation_reports/bz/3bzg | HTTPS FTP |
-Related structure data
Related structure data | 3bzjC 3c0lC 3c0qC 3c0sC 2j6vS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33983.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q746K1 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.4 Details: Acetate, Naformate, MnCl2, pH4.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: MAR225 / Detector: CCD / Date: Jul 16, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→92.848 Å / Num. obs: 24142 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.91→2.01 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.282 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J6V Resolution: 1.91→28.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.448 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.159 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 25.794 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→28.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.959 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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