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- PDB-5d5c: In meso in situ serial X-ray crystallography structure of lysozym... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d5c | ||||||
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Title | In meso in situ serial X-ray crystallography structure of lysozyme at 100 K | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Huang, C.-Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, M. / Caffrey, 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 | ![]() | 44.1 KB | Display | ![]() |
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PDB format | ![]() | 28.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 662.6 KB | Display | ![]() |
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Full document | ![]() | 662.8 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d52C ![]() 5d53C ![]() 5d54C ![]() 5d56C ![]() 5d57C ![]() 5d58C ![]() 5d59C ![]() 5d5aC ![]() 5d5bC ![]() 5d5dC ![]() 5d5eC ![]() 5d5fC ![]() 3tmuS 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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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 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 107 molecules 








#2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-ACY / | #5: Chemical | ChemComp-PE5 / | #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.21 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.5-1 M NaBr, 50-100 mM CH3COONa, pH 4.5, and 15-30 %(v/v) PEG400 PH range: pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 13594 / % possible obs: 99.7 % / Redundancy: 5.5 % / Net I/σ(I): 6.16 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3tmu Resolution: 1.7→39.545 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→39.545 Å
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Refine LS restraints |
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LS refinement shell |
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