+Open data
-Basic information
Entry | Database: PDB / ID: 5h99 | |||||||||||||||
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Title | Crystal structure of Geobacter metallireducens SMUG1 mutant N58D | |||||||||||||||
Components | Geobacter metallireducens SMUG1 | |||||||||||||||
Keywords | HYDROLASE / SMUG1 / DNA damage / base excision repair / substrate specificity | |||||||||||||||
Function / homology | Function and homology information single-strand selective uracil DNA N-glycosylase activity / base-excision repair / DNA binding Similarity search - Function | |||||||||||||||
Biological species | Geobacter metallireducens (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||||||||
Authors | Xie, W. / Cao, W. / Zhang, Z. / Shen, J. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Structural Basis of Substrate Specificity in Geobacter metallireducens SMUG1 Authors: Zhang, Z. / Shen, J. / Yang, Y. / Li, J. / Cao, W. / Xie, W. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h99.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h99.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 5h99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/5h99 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/5h99 | HTTPS FTP |
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-Related structure data
Related structure data | 5h93C 5h98C 5h9iC 1oe4S 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26127.936 Da / Num. of mol.: 2 / Mutation: N58D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria) Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: Gmet_0095 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q39ZI0 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 16-21% PEG6000, 0.2M NaCl or (NH4)2SO4 and 0.1M MES (pH 6.0) |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Nov 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25.7 Å / Num. obs: 15442 / % possible obs: 99.5 % / Observed criterion σ(I): 2.4 / Redundancy: 3.6 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.4 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OE4 Resolution: 2.5→25.7 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→25.7 Å
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Refine LS restraints |
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LS refinement shell |
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