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Yorodumi- PDB-3txi: HEWL co-crystallization with carboplatin in DMSO media with parat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3txi | ||||||
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Title | HEWL co-crystallization with carboplatin in DMSO media with paratone as the cryoprotectant | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / hen egg white lysozyme (HEWL) / bacterial cell wall lysis | ||||||
Function / homology | Function and homology information 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 | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Tanley, S.W.M. / Schreurs, A.M.M. / Helliwell, J.R. / Kroon-Batenburg, L.M.J. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3txi.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3txi.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 3txi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3txi_validation.pdf.gz | 462.8 KB | Display | wwPDB validaton report |
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Full document | 3txi_full_validation.pdf.gz | 464.7 KB | Display | |
Data in XML | 3txi_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 3txi_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/3txi ftp://data.pdbj.org/pub/pdb/validation_reports/tx/3txi | HTTPS FTP |
-Related structure data
Related structure data | 3txbC 3txdC 3txeC 3txfC 3txgC 3txhC 3txjC 3txkC 2w1yS 3txc 3txl C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme |
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-Non-polymers , 5 types, 139 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Chemical | ChemComp-DMS / #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.34 % |
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Crystal grow | Temperature: 295 K / Method: batch / pH: 4.7 Details: 49 mg HEWL + 3.7 mg carboplatin 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 31, 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: 1.6→55.18 Å / Num. all: 15587 / Num. obs: 14573 / % possible obs: 93.5 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 23.27 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 7.38 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.2 / Num. unique all: 15587 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W1Y Resolution: 1.6→55.17 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.839 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R: 0.107 / ESU R Free: 0.109 / 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: 29.925 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→55.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -20.1003 Å / Origin y: -0.7753 Å / Origin z: -8.6806 Å
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