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Yorodumi- PDB-6jtl: Crystal structure of NagZ from Neisseria gonorrhoeae in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jtl | ||||||
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Title | Crystal structure of NagZ from Neisseria gonorrhoeae in complex with zinc ion | ||||||
Components | Beta-hexosaminidase | ||||||
Keywords | HYDROLASE / Neisseria gonorrhoeae / acetylglucosaminidase / peptidoglycan recycling | ||||||
Function / homology | Function and homology information beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Chen, Y. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of NagZ from Neisseria gonorrhoeae in complex with zinc ion Authors: Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jtl.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jtl.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jtl_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6jtl_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6jtl_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 6jtl_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/6jtl ftp://data.pdbj.org/pub/pdb/validation_reports/jt/6jtl | HTTPS FTP |
-Related structure data
Related structure data | 6jtiS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 3 - 347 / Label seq-ID: 39 - 383
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-Components
#1: Protein | Mass: 42905.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: nagZ, NGO0135 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5FA94, beta-N-acetylhexosaminidase #2: Chemical | ChemComp-ZN / #3: 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: 1.86 Å3/Da / Density % sol: 33.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Sodium acetate trihydrate, 20% w/v polyethylene glycol 3,350 pH8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 25780 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1244 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JTI Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.659 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.675 / ESU R Free: 0.285 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.887 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→50 Å
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Refine LS restraints |
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