+Open data
-Basic information
Entry | Database: PDB / ID: 6rt1 | ||||||
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Title | Native tetragonal lysozyme - home source data | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Glycoside hydrolase | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 / MOLECULAR REPLACEMENT / Resolution: 1.336 Å | ||||||
Authors | Pereira, P.J.B. | ||||||
Citation | Journal: Phys Chem Chem Phys / Year: 2020 Title: Protein crystals as a key for deciphering macromolecular crowding effects on biological reactions. Authors: Ferreira, C. / Pinto, M.F. / Macedo-Ribeiro, S. / Pereira, P.J.B. / Rocha, F.A. / Martins, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rt1.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rt1.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 6rt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rt1_validation.pdf.gz | 429.5 KB | Display | wwPDB validaton report |
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Full document | 6rt1_full_validation.pdf.gz | 429.5 KB | Display | |
Data in XML | 6rt1_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 6rt1_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/6rt1 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/6rt1 | HTTPS FTP |
-Related structure data
Related structure data | 6rt3C 6rt9C 6rtaC 2w1xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/654 / Data set type: diffraction image data |
-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, lysozyme | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 100 mM Sodium Acetate pH 4.8, 10% (w/v) NaCl, 25% (v/v) Ethylene Glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION GEMINI / Wavelength: 1.54056 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Jun 24, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 1.336→14.602 Å / Num. obs: 26070 / % possible obs: 96.9 % / Redundancy: 20.8 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.014 / Rrim(I) all: 0.069 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.34→1.36 Å / Num. unique obs: 655 / % possible all: 50.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W1X Resolution: 1.336→14.602 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.336→14.602 Å
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Refine LS restraints |
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LS refinement shell |
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