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- PDB-4yem: Carboplatin binding to HEWL in NaBr crystallisation conditions st... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yem | ||||||
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Title | Carboplatin binding to HEWL in NaBr crystallisation conditions studied at an X-ray wavelength of 0.9163A - new refinement | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / Re-refinement of 4XAN / Carboplatin / Metal binding / lysozyme | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Shabalin, I.G. / Dauter, Z. / Jaskolski, M. / Minor, W. / Wlodawer, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin. Authors: Shabalin, I. / Dauter, Z. / Jaskolski, M. / Minor, W. / Wlodawer, A. #1: ![]() Title: Carboplatin binding to histidine. Authors: Tanley, S.W. / Diederichs, K. / Kroon-Batenburg, L.M. / Levy, C. / Schreurs, A.M. / Helliwell, J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.1 KB | Display | ![]() |
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PDB format | ![]() | 57.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ydxC ![]() 4yeaC ![]() 4yenC ![]() 4yeoC ![]() 4xan S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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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) ![]() ![]() |
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-Non-polymers , 7 types, 204 molecules ![](data/chem/img/PT.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-BR / #4: Chemical | ChemComp-NA / | #5: Chemical | #6: Chemical | ChemComp-ACT / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.76 % |
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Crystal grow | Temperature: 297 K / Method: batch mode / pH: 4.7 Details: co-crystallizing 20 mg ml HEWL with 1.4 mg carboplatin in 75 ml DMSO, 462.5 ml 0.1 M sodium acetate, 462.5 ml 1 M NaBr solution. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2013 |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9163 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→55.56 Å / Num. all: 18627 / Num. obs: 17672 / % possible obs: 94.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.2 / % possible all: 64 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XAN ![]() 4xan Resolution: 1.47→39.29 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1545 / WRfactor Rwork: 0.1032 / FOM work R set: 0.9142 / SU B: 2.228 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0743 / SU Rfree: 0.0648 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY This deposit resulted from an analysis of a number of PDB entries that contain cisplatin or carboplatin in ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY This deposit resulted from an analysis of a number of PDB entries that contain cisplatin or carboplatin in complex with proteins, conducted in the spirit of the Terwilliger-Bricogne motto advocating continuous improvement of the macromolecular models in the PDB (Acta Cryst. D70, 2533, 2014). The structure factors and coordinates, originally deposited as 4xan (4nsf), were used as the starting point for an independent re-refinement. The new model includes some reinterpretation of the ligands, has lower R factors, and improved statistics describing the agreement with the experimental data.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.86 Å2 / Biso mean: 14.86 Å2 / Biso min: 6.09 Å2
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Refinement step | Cycle: final / Resolution: 1.47→39.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.508 Å / Total num. of bins used: 20
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