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Yorodumi- PDB-8aaz: High resolution X-ray analysis of ATP lysozyme complex in the pre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aaz | ||||||
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Title | High resolution X-ray analysis of ATP lysozyme complex in the presence of 80 mM ATP | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Complex / ligand binding / ATP / lysozyme | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å | ||||||
Authors | Zalar, M. / Curtis, R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Nonspecific Binding of Adenosine Tripolyphosphate and Tripolyphosphate Modulates the Phase Behavior of Lysozyme. Authors: Zalar, M. / Bye, J. / Curtis, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aaz.cif.gz | 120.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aaz.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 8aaz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/8aaz ftp://data.pdbj.org/pub/pdb/validation_reports/aa/8aaz | HTTPS FTP |
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-Related structure data
Related structure data | 2lztS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.79 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10 mM Tris-HCl pH 7.0, 80 mM Na2-ATP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→39.19 Å / Num. obs: 31931 / % possible obs: 99.99 % / Redundancy: 51.6 % / Biso Wilson estimate: 12.22 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0516 / Rpim(I) all: 0.007296 / Rrim(I) all: 0.05213 / Net I/σ(I): 50.22 |
Reflection shell | Resolution: 1.27→1.315 Å / Redundancy: 50.9 % / Rmerge(I) obs: 0.2322 / Mean I/σ(I) obs: 10.3 / Num. unique obs: 3125 / CC1/2: 0.993 / CC star: 0.998 / Rpim(I) all: 0.03279 / Rrim(I) all: 0.2346 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LZT Resolution: 1.27→39.19 Å / SU ML: 0.1038 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 14.4983 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.27→39.19 Å
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Refine LS restraints |
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LS refinement shell |
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