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Yorodumi- PDB-1zbk: Recognition of specific peptide sequences by signalling protein f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zbk | ||||||
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Title | Recognition of specific peptide sequences by signalling protein from sheep mammary gland (SPS-40): Crystal structure of the complex of SPS-40 with a peptide Trp-Pro-Trp at 2.9A resolution | ||||||
Components |
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Keywords | SIGNALING PROTEIN / SPS-40 / WPW | ||||||
Function / homology | Function and homology information response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitinase activity / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / lung development / positive regulation of peptidyl-threonine phosphorylation ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitinase activity / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / lung development / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / carbohydrate metabolic process / inflammatory response / apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / cytoplasm Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Srivastava, D.B. / Ethayathulla, A.S. / Kumar, J. / Singh, N. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Recognition of specific peptide sequences by signalling protein from sheep mammary gland (SPS-40): Crystal structure of the complex of SPS-40 with a peptide Trp-Pro-Trp at 2.9A resolution Authors: Srivastava, D.B. / Ethayathulla, A.S. / Kumar, J. / Singh, N. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zbk.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zbk.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zbk_validation.pdf.gz | 397.2 KB | Display | wwPDB validaton report |
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Full document | 1zbk_full_validation.pdf.gz | 409.5 KB | Display | |
Data in XML | 1zbk_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1zbk_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/1zbk ftp://data.pdbj.org/pub/pdb/validation_reports/zb/1zbk | HTTPS FTP |
-Related structure data
Related structure data | 1r2v 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
#1: Protein | Mass: 40612.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Tissue: Mammary glands / References: UniProt: Q6TMG6 | ||
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#2: Protein/peptide | Mass: 487.550 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED USING Trp-Pro-Trp SOLIDE PHASE PEPTIDE SYNTHESIS | ||
#3: Sugar | #4: 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: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 25mM tris-HCl, 11% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 14, 2004 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→56 Å / Num. all: 10552 / Num. obs: 9982 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35 Å2 / Rsym value: 0.19 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.9→3 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.66 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1r2v 1r2v Resolution: 2.9→56 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.54 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.07 Å / Rfactor Rfree error: 0.06
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