+Open data
-Basic information
Entry | Database: PDB / ID: 8u6x | ||||||
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Title | ATP-dependent DNA ligase Lig E from Neisseria gonorrhoeae | ||||||
Components |
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Keywords | LIGASE/DNA / enzyme-adenylate / Lig E / LIGASE / LIGASE-DNA complex | ||||||
Function / homology | Function and homology information DNA ligase (ATP) activity / DNA recombination / DNA repair / ATP binding Similarity search - Function | ||||||
Biological species | Neisseria gonorrhoeae MS11 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Williamson, A. / Pan, J. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: Bmc Microbiol. / Year: 2024 Title: A role for the ATP-dependent DNA ligase lig E of Neisseria gonorrhoeae in biofilm formation. Authors: Pan, J. / Singh, A. / Hanning, K. / Hicks, J. / Williamson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u6x.cif.gz | 147 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u6x.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 8u6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u6x_validation.pdf.gz | 745.9 KB | Display | wwPDB validaton report |
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Full document | 8u6x_full_validation.pdf.gz | 746.9 KB | Display | |
Data in XML | 8u6x_validation.xml.gz | 12 KB | Display | |
Data in CIF | 8u6x_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/8u6x ftp://data.pdbj.org/pub/pdb/validation_reports/u6/8u6x | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32029.357 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae MS11 (bacteria) / Gene: NGFG_01849 / Plasmid: pDEST 17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: D6HB39 |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 6494.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 6392.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 46 molecules
#4: Chemical | ChemComp-AMP / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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 Å3/Da / Density % sol: 59.1 % / Description: small rods/ plates |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.5 M potassium thiocyanate, 0.1 M Bis Tris Propane pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953724 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953724 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→48.93 Å / Num. obs: 13286 / % possible obs: 99.86 % / Redundancy: 8.7 % / Biso Wilson estimate: 53.06 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1076 / Rpim(I) all: 0.03774 / Rrim(I) all: 0.1144 / Net I/σ(I): 11.88 |
Reflection shell | Resolution: 2.44→2.527 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 1269 / CC1/2: 0.694 / CC star: 0.905 / Rpim(I) all: 0.3757 / Rrim(I) all: 1.146 / % possible all: 99.61 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→48.93 Å / SU ML: 0.3919 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.9417 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.44→48.93 Å
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Refine LS restraints |
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LS refinement shell |
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