+Open data
-Basic information
Entry | Database: PDB / ID: 8w6k | ||||||
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Title | in situ room temperature Laue crystallography | ||||||
Components | Lysozyme C | ||||||
Keywords | LYASE / Complex | ||||||
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 | Asplenium bulbiferum subsp. bulbiferum (hen and chickens fern) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wang, Z.J. / Wang, S.S. / Pan, Q.Y. / Yu, L. / Su, Z.H. / Yang, T.Y. / Wang, Y.Z. / Zhang, W.Z. / Hao, Q. / Gao, X.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: BL03HB: Laue crystallography beamline at SSRF Authors: Wang, Z.J. / Wang, S.S. / Pan, Q.Y. / Yu, L. / Su, Z.H. / Yang, T.Y. / Wang, Y.Z. / Zhang, W.Z. / Wang, Q.S. / Hao, Q. / Gao, X.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w6k.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w6k.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 8w6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8w6k_validation.pdf.gz | 404.3 KB | Display | wwPDB validaton report |
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Full document | 8w6k_full_validation.pdf.gz | 406.6 KB | Display | |
Data in XML | 8w6k_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 8w6k_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/8w6k ftp://data.pdbj.org/pub/pdb/validation_reports/w6/8w6k | HTTPS FTP |
-Related structure data
Related structure data | 8y1rC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Asplenium bulbiferum subsp. bulbiferum (hen and chickens fern) References: UniProt: P00698 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.07 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: sodium acetate buffer, pH 4.55, and sodium chloride Temp details: 293 |
-Data collection
Diffraction | Mean temperature: 293 K / Ambient temp details: 293 / Serial crystal experiment: Y | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL03HB / Wavelength: 0.6 - 1.7 | |||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 16, 2023 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→19 Å / Num. obs: 3771 / % possible obs: 68 % / Redundancy: 1 % / CC1/2: 0.582 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.165 / Χ2: 0.76 / Net I/σ(I): 7.3 | |||||||||
Reflection shell | Resolution: 1.99→16.9 Å / Rmerge(I) obs: 0.156 / Num. unique obs: 1040 / CC1/2: 0.791 / % possible all: 43.7 | |||||||||
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→16.99 Å / SU ML: 0.57 / Cross valid method: NONE / σ(F): 1.61 / Phase error: 39.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→16.99 Å
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Refine LS restraints |
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LS refinement shell |
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