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- PDB-4z8i: Crystal structure of Branchiostoma belcheri tsingtauense peptidog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4z8i | |||||||||||||||
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Title | Crystal structure of Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3 | |||||||||||||||
![]() | peptidoglycan recognition protein 3 | |||||||||||||||
![]() | HYDROLASE / peptidoglycan recognition protein / chitin-binding domain / amidase | |||||||||||||||
Function / homology | ![]() N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / immune system process / chitin binding / peptidoglycan catabolic process / zinc ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Wang, W.J. / Cheng, W. / Jiang, Y.L. / Luo, M. / Cao, D.D. / Chi, C.B. / Yang, H.B. / Chen, Y. / Zhou, C.Z. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Activity Augmentation of Amphioxus Peptidoglycan Recognition Protein BbtPGRP3 via Fusion with a Chitin Binding Domain Authors: Wang, W.J. / Cheng, W. / Luo, M. / Yan, Q. / Yu, H.M. / Li, Q. / Cao, D.D. / Huang, S. / Xu, A. / Mariuzza, R.A. / Chen, Y. / Zhou, C.Z. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.2 KB | Display | ![]() |
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PDB format | ![]() | 77 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.1 KB | Display | ![]() |
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Full document | ![]() | 423.6 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zxmC ![]() 1ohtS 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
#1: Protein | Mass: 25450.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pAcGP67 / Cell line (production host): Sf9 / Production host: ![]() ![]() References: UniProt: A0A0R4I979*PLUS, N-acetylmuramoyl-L-alanine amidase |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.95 % Description: the entry contains Friedel pairs in F_Plus/Minus columns |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.2 M Lithium sulfate, 0.1 M Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97886 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 15022 / % possible obs: 99.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OHT Resolution: 2.701→38.603 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.56 / Stereochemistry target values: ML Details: the entry contains Friedel pairs in F_Plus/Minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.701→38.603 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -33.8329 Å / Origin y: 11.8014 Å / Origin z: 19.6129 Å
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Refinement TLS group | Selection details: all |