+Open data
-Basic information
Entry | Database: PDB / ID: 207l | ||||||
---|---|---|---|---|---|---|---|
Title | MUTANT HUMAN LYSOZYME C77A | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE (O-GLYCOSYL)-CYS) / MUTANT HUMAN LYSOZYME / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information metabolic process / cytolysis / antimicrobial humoral response / retina homeostasis / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity ...metabolic process / cytolysis / antimicrobial humoral response / retina homeostasis / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Matsushima, M. / Song, H. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 1996 Title: A role of PDI in the reductive cleavage of mixed disulfides. Authors: Nakamura, S. / Matsushima, M. / Song, H. / Kikuchi, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Structure of a Glutathionylated Human Lysozyme: A Folding Intermediate Mimic in the Formation of a Disulfide Bond Authors: Inaka, K. / Miki, K. / Kikuchi, M. / Taniyama, Y. / Matsushima, M. #2: Journal: FEBS Lett. / Year: 1993 Title: Pdi and Glutathione-Mediated Reduction of the Glutathionylated Variant of Human Lysozyme Authors: Hayano, T. / Inaka, K. / Otsu, M. / Taniyama, Y. / Miki, K. / Matsushima, M. / Kikuchi, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 207l.cif.gz | 41.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb207l.ent.gz | 28.1 KB | Display | PDB format |
PDBx/mmJSON format | 207l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 207l_validation.pdf.gz | 382.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 207l_full_validation.pdf.gz | 384.2 KB | Display | |
Data in XML | 207l_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 207l_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/07/207l ftp://data.pdbj.org/pub/pdb/validation_reports/07/207l | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14688.627 Da / Num. of mol.: 1 / Mutation: C77A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00695, UniProt: P61626*PLUS, lysozyme |
---|---|
#2: Chemical | ChemComp-SC2 / |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.72 % Description: INDEPENDENTLY REREFINED HUMAN LYSOZYME AT 1.5 A RESOLUTION BY PROLSQ | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 280 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 1, 1993 / Details: MIRROR-MIRROR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→100 Å / Num. obs: 8903 / % possible obs: 75.3 % / Observed criterion σ(I): 2 / Redundancy: 2.68 % / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 1.75→1.78 Å / % possible all: 42.2 |
Reflection shell | *PLUS % possible obs: 42.2 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NATIVE HUMAN LYSOZYME Resolution: 1.8→6 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |