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- PDB-3txe: HEWL co-crystallization with carboplatin in aqueous media with pa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3txe | ||||||
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Title | HEWL co-crystallization with carboplatin in aqueous 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 | ![]() | 44 KB | Display | ![]() |
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PDB format | ![]() | 29 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.7 KB | Display | ![]() |
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Full document | ![]() | 445.6 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3txbC ![]() 3txdC ![]() 3txfC ![]() 3txgC ![]() 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
#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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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-MEB / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.88 % |
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Crystal grow | Temperature: 295 K / Method: batch / pH: 4.7 Details: 49 mg HEWL + 3.7 mg carboplatin in 1 mL 0.04 M sodium acetate + 1 mL 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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 17, 2011 / Details: Osmic Confocal Max-Flux, blue configuration |
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→55.51 Å / Num. all: 13378 / Num. obs: 12432 / % possible obs: 92.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 18.99 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 14.01 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 4.2 / Num. unique all: 13378 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2W1Y Resolution: 1.7→55.51 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.901 / SU B: 2.985 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R: 0.135 / ESU R Free: 0.138 / 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: 31.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→55.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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