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- PDB-3txg: HEWL co-crystallization with cisplatin in DMSO media with paraton... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3txg | ||||||
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Title | HEWL co-crystallization with cisplatin in DMSO media with paratone as the cryoprotectant | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / hen egg white lysozyme (HEWL) / bacterial cell wall lysis | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tanley, S.W.M. / Schreurs, A.M.M. / Helliwell, J.R. / Kroon-Batenburg, L.M.J. | ||||||
![]() | ![]() Title: Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals. Authors: Tanley, S.W. / Schreurs, A.M. / Helliwell, J.R. / Kroon-Batenburg, L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.8 KB | Display | ![]() |
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PDB format | ![]() | 50.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.2 KB | Display | ![]() |
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Full document | ![]() | 470.3 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3txbC ![]() 3txdC ![]() 3txeC ![]() 3txfC ![]() 3txhC ![]() 3txiC ![]() 3txjC ![]() 3txkC ![]() 2w1yS ![]() 3txc ![]() 3txl C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 124 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CPT.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CPT.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Chemical | ChemComp-DMS / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.66 % |
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Crystal grow | Temperature: 295 K / Method: batch / pH: 4.7 Details: 49 mg HEWL + 3 mg cisplatin in 462.5 uL 0.04 M sodium acetate + 75 uL DMSO + 462.5 uL 10% sodium chloride, with paratone as cryoprotectant, pH 4.7, BATCH, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Nov 25, 2010 / Details: Incoatec Helios confocal optics |
Radiation | Monochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37.1 Å / Num. all: 13147 / Num. obs: 12342 / % possible obs: 93.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 24.27 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.023 / Rsym value: 0.023 / Net I/σ(I): 25.66 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 16.21 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 4.02 / Num. unique all: 13147 / % possible all: 97.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2W1Y Resolution: 1.7→34.92 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.702 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R: 0.124 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.939 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→34.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.743 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -20.0496 Å / Origin y: -0.9446 Å / Origin z: -8.8274 Å
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