+Open data
-Basic information
Entry | Database: PDB / ID: 6ro3 | ||||||
---|---|---|---|---|---|---|---|
Title | 2Yr-X: Lysozyme with Re Cluster 2 year on shelf | ||||||
Components | Lysozyme C | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Radio-pharmaceuticals / organometallic complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.03 Å | ||||||
Authors | Brink, A. / Helliwell, J.R. | ||||||
Funding support | South Africa, 1items
| ||||||
Citation | Journal: Iucrj / Year: 2019 Title: Formation of a highly dense tetra-rhenium cluster in a protein crystal and its implications in medical imaging. Authors: Brink, A. / Helliwell, J.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ro3.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ro3.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ro3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/6ro3 ftp://data.pdbj.org/pub/pdb/validation_reports/ro/6ro3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ro5C 2w1yS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#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 |
---|
-Non-polymers , 8 types, 135 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-BR / | #8: Chemical | ChemComp-ACT / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.48 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: Standard hen egg white lysozyme (20 mg) crystallisation conditions were used of 10% NaCl, NaOAc 0.04 M (pH 4.7) and the fac-[Et4N]2[Re(CO)3(Br)3] at 0.03 M in 1.4 ml water, in sitting drop ...Details: Standard hen egg white lysozyme (20 mg) crystallisation conditions were used of 10% NaCl, NaOAc 0.04 M (pH 4.7) and the fac-[Et4N]2[Re(CO)3(Br)3] at 0.03 M in 1.4 ml water, in sitting drop conditions, initially included with DMSO (at 7.5 % v/v). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→39.97 Å / Num. obs: 55335 / % possible obs: 94.04 % / Redundancy: 11.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 1.03→1.067 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.1646 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3732 / CC1/2: 0.897 / % possible all: 64.31 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W1Y Resolution: 1.03→39.97 Å / SU ML: 0.04 / SU R Cruickshank DPI: 0.018 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 7.91
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.03→39.97 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|