+Open data
-Basic information
Entry | Database: PDB / ID: 4lzt | ||||||
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Title | ATOMIC RESOLUTION REFINEMENT OF TRICLINIC HEW LYSOZYME AT 295K | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / O-GLYCOSYL / GLYCOSIDASE | ||||||
Function / homology | Function and homology information 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 ...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 / STRUCTURE KNOWN / Resolution: 0.95 Å | ||||||
Authors | Walsh, M.A. / Schneider, T. / Sieker, L.C. / Dauter, Z. / Lamzin, V. / Wilson, K.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Refinement of triclinic hen egg-white lysozyme at atomic resolution. Authors: Walsh, M.A. / Schneider, T.R. / Sieker, L.C. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1990 Title: Refinement of Triclinic Lysozyme: I. Fourier and Least-Squares Methods Authors: Hodsdon, J.M. / Brown, G.M. / Sieker, L.C. / Jensen, L.H. #2: Journal: Acta Crystallogr.,Sect.B / Year: 1990 Title: Refinement of Triclinic Lysozyme: II. The Method of Stereochemically Restrained Least Squares Authors: Ramanadham, M. / Sieker, L.C. / Jensen, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lzt.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lzt.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 4lzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/4lzt ftp://data.pdbj.org/pub/pdb/validation_reports/lz/4lzt | HTTPS FTP |
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-Related structure data
Related structure data | 3lztC 2lztS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NITRATE IONS PRESENT / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / References: UniProt: P00698, lysozyme | ||
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#2: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 31.8 % | ||||||||||||||||||||
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Crystal grow | Method: batch method / pH: 4.5 Details: BATCH METHOD USED. 1% PROTEIN SOLUTION IN 100MM SODIUM ACETATE PH 4.5-4.6. SODIUM NITRATE ADDED TO A CONCENTRATION OF 20MGS/ML. CRYSTALS GROWN AT ROOM TEMPERATURE., batch method PH range: 4.5-4.6 / Temp details: room temp | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 296 K / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.862 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.862 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→21 Å / Num. obs: 61265 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 0.95→0.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.273 / % possible all: 94.9 |
Reflection | *PLUS Num. measured all: 289540 |
Reflection shell | *PLUS % possible obs: 94.9 % |
-Processing
Software |
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Refinement | Method to determine structure: STRUCTURE KNOWN Starting model: PDB ENTRY 2LZT Resolution: 0.95→21 Å / Num. parameters: 10801 / Num. restraintsaints: 13288 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER Details: WATER OCCUPANCIES REFINED DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 15 / Occupancy sum hydrogen: 920.89 / Occupancy sum non hydrogen: 1123.7 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→21 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.147 / Rfactor Rwork: 0.1144 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |