+Open data
-Basic information
Entry | Database: PDB / ID: 1qud | ||||||
---|---|---|---|---|---|---|---|
Title | L99G MUTANT OF T4 LYSOZYME | ||||||
Components | PROTEIN (LYSOZYME) | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.75 Å | ||||||
Authors | Wray, J. / Baase, W.A. / Lindstrom, J.D. / Poteete, A.R. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Structural analysis of a non-contiguous second-site revertant in T4 lysozyme shows that increasing the rigidity of a protein can enhance its stability. Authors: Wray, J.W. / Baase, W.A. / Lindstrom, J.D. / Weaver, L.H. / Poteete, A.R. / Matthews, B.W. #1: Journal: J.Mol.Biol. / Year: 1987 Title: Structure of Bacteriophage T4 Lysozyme Refined at 1.7A Resolution Authors: Weaver, L.H. / Matthews, B.W. #2: Journal: Biochemistry / Year: 1991 Title: Second-site Revertants of an Inactive T4 Lysozyme Mutant Restore Activity Structuring the Active Site Cleft Authors: Poteete, A.R. / Sun, D.P. / Nicholson, H. / Matthews, B.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qud.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qud.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 1qud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qud_validation.pdf.gz | 428.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1qud_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 1qud_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 1qud_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/1qud ftp://data.pdbj.org/pub/pdb/validation_reports/qu/1qud | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18344.996 Da / Num. of mol.: 1 / Mutation: C54T, C97A, L99G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Plasmid: M13 PHS1403 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-HEZ / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.69 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 7.1 / PH range high: 6.3 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
---|---|
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. all: 49752 / Num. obs: 20715 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.75→1.88 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.224 / Num. unique all: 3808 / % possible all: 89 |
Reflection shell | *PLUS % possible obs: 89 % |
-Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.75→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
| ||||||||||||
Refine LS restraints |
|