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Yorodumi- PDB-4qh0: Crystal structure of NucA from Streptococcus agalactiae with magn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qh0 | ||||||
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Title | Crystal structure of NucA from Streptococcus agalactiae with magnesium ion bound | ||||||
Components | DNA-entry nuclease (Competence-specific nuclease) | ||||||
Keywords | HYDROLASE / Nuclease / beta beta alpha metal finger / virulence factor | ||||||
Function / homology | Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Streptococcus agalactiae ILRI112 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Moon, A.F. / Gaudu, P. / Pedersen, L.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural characterization of the virulence factor nuclease A from Streptococcus agalactiae. Authors: Moon, A.F. / Gaudu, P. / Pedersen, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qh0.cif.gz | 203.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qh0.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 4qh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/4qh0 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/4qh0 | HTTPS FTP |
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-Related structure data
Related structure data | 4qgoSC 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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 25239.607 Da / Num. of mol.: 4 / Fragment: catalytic domain / Mutation: H148A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae ILRI112 (bacteria) Gene: SAIL_8320 / Production host: Escherichia coli (E. coli) / References: UniProt: R5A2Y6 |
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-Non-polymers , 5 types, 805 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / #5: Chemical | #6: 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: 3.44 Å3/Da / Density % sol: 64.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50mM Tris, 1.6M, ammonium sulfate, 10mM MgCl2 and 1:136 molar ratio of protein to 8mer duplex of 5'-GCGATCGC-3' DNA (not visible in structure), VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Feb 26, 2014 / Details: VariMaxHF |
Radiation | Monochromator: VariMaxHF Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 89816 / Num. obs: 89816 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rsym value: 0.08 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 7329 / Rsym value: 0.33 / % possible all: 79.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4QGO Resolution: 2→24.854 Å / σ(F): 1.33 / Phase error: 25.61 / Stereochemistry target values: TWIN_LSQ_F
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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→24.854 Å
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Refine LS restraints |
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LS refinement shell |
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