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- PDB-3cxm: Leishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cxm | ||||||
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Title | Leishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil | ||||||
![]() | Uracil-DNA glycosylase | ||||||
![]() | HYDROLASE / base excision repair / BER / DNA damage repair / Leishmania / MSGPP / SGPP / glycosylase / 5-bromouracil / Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / DNA repair / Glycosidase / PSI-2 / Protein Structure Initiative | ||||||
Function / homology | ![]() uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / mitochondrion / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Larson, E.T. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP) | ||||||
![]() | ![]() Title: Structures of Leishmania naiffi uracil-DNA glycosylase in complex with several ligands identified with fragment cocktail crystallography. Authors: Larson, E.T. / Merritt, E.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.4 KB | Display | ![]() |
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PDB format | ![]() | 53 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1euiS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30285.660 Da / Num. of mol.: 1 / Fragment: Residues 129-373 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: D0VWU0*PLUS, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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-Non-polymers , 5 types, 244 molecules ![](data/chem/img/BR.gif)
![](data/chem/img/URB.gif)
![](data/chem/img/URA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/URB.gif)
![](data/chem/img/URA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-BR / |
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#3: Chemical | ChemComp-URB / |
#4: Chemical | ChemComp-URA / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | 1. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...1. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.96 % Description: 1. The Blu-ice software package was used for data collection. The reference is: McPhillips T.M., McPhillips S.E., Chiu H.J., Cohen A.E., Deacon A.M., Ellis P.J., Garman E., Gonzalez A., ...Description: 1. The Blu-ice software package was used for data collection. The reference is: McPhillips T.M., McPhillips S.E., Chiu H.J., Cohen A.E., Deacon A.M., Ellis P.J., Garman E., Gonzalez A., Sauter N.K., Phizackerley R.P., Soltis S.M., Kuhn P., Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. J.Synchrotron Radiat. 2002 Nov 1, 9(Pt 6):401-6. Epub 2002 Nov 1. PMID: 12409628. 2. The TLS motion determination server (http://skuld.bmsc.washington.edu/~tlsmd/) was used for selection of the TLS groups used in refinement. The reference is: Painter J. and Merritt E.A., TLSMD web server for the generation of multi-group TLS models. J.Appl.Cryst. 2006 Feb, 39(Pt 1):109-111. Epub 2006 Jan 12. |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.3 M Potassium phosphate dibasic, 0.1 M Sodium acetate pH 4.5, 5 mM DTT, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 28, 2007 / Details: Mirrors |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91724 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 52821 / % possible obs: 97.2 % / Redundancy: 10.2 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.045 / Χ2: 0.978 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4325 / Χ2: 0.979 / % possible all: 79.9 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1EUI Resolution: 1.5→37.66 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.155 / WRfactor Rwork: 0.133 / SU B: 2.276 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 2. 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.353 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→37.66 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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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