+Open data
-Basic information
Entry | Database: PDB / ID: 1oht | ||||||
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Title | Peptidoglycan recognition protein LB | ||||||
Components | CG14704 PROTEIN | ||||||
Keywords | HYDROLASE / PEPTIDOGLYCAN-RECOGNITION PROTEIN-LB ISOFORM 2 | ||||||
Function / homology | Function and homology information negative regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria / Antimicrobial peptides / negative regulation of peptidoglycan recognition protein signaling pathway / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / peptidoglycan catabolic process / defense response to Gram-positive bacterium / innate immune response / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å | ||||||
Authors | Kim, M.-S. / Byun, M. / Oh, B.-H. | ||||||
Citation | Journal: Nat.Immunol. / Year: 2003 Title: Crystal Structure of Peptidoglycan Recognition Protein Lb from Drosophila Melanogaster Authors: Kim, M.-S. / Byun, M. / Oh, B.-H. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oht.cif.gz | 45.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oht.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 1oht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oht_validation.pdf.gz | 456.6 KB | Display | wwPDB validaton report |
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Full document | 1oht_full_validation.pdf.gz | 458.2 KB | Display | |
Data in XML | 1oht_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 1oht_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/1oht ftp://data.pdbj.org/pub/pdb/validation_reports/oh/1oht | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23961.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9VGN3, UniProt: Q8INK6*PLUS | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Chemical | ChemComp-TLA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||
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Crystal grow | *PLUS Temperature: 14 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97921 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 12443 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 44 % |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 88.2 % / Rmerge(I) obs: 0.201 |
-Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SIRAS / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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