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- PDB-4ynl: Crystal structure of the hood domain of Anabaena HetR in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ynl | |||||||||
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Title | Crystal structure of the hood domain of Anabaena HetR in complex with the hexapeptide ERGSGR derived from PatS | |||||||||
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![]() | TRANSCRIPTION / Heterocyst differentiation / Transcription factor | |||||||||
Function / homology | ![]() heterocyst development / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / periplasmic space / serine-type endopeptidase activity / proteolysis / DNA binding / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hu, H.X. / Jiang, Y.L. / Zhao, M.X. / Zhang, C.C. / Chen, Y. / Zhou, C.Z. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into HetR-PatS interaction involved in cyanobacterial pattern formation Authors: Hu, H.X. / Jiang, Y.L. / Zhao, M.X. / Cai, K. / Liu, S. / Wen, B. / Lv, P. / Zhang, Y. / Peng, J. / Zhong, H. / Yu, H.M. / Ren, Y.M. / Zhang, Z. / Tian, C. / Wu, Q. / Oliveberg, M. / Zhang, ...Authors: Hu, H.X. / Jiang, Y.L. / Zhao, M.X. / Cai, K. / Liu, S. / Wen, B. / Lv, P. / Zhang, Y. / Peng, J. / Zhong, H. / Yu, H.M. / Ren, Y.M. / Zhang, Z. / Tian, C. / Wu, Q. / Oliveberg, M. / Zhang, C.C. / 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 | ![]() | 85.5 KB | Display | ![]() |
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PDB format | ![]() | 64.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.5 KB | Display | ![]() |
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Full document | ![]() | 485.1 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yrvC ![]() 4k1m C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10997.505 Da / Num. of mol.: 4 / Fragment: UNP residues 219-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 662.698 Da / Num. of mol.: 4 / Fragment: UNP residues 12-17 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.11 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 25% PEG 4000, 0.1 M sodium citrate, 0.2 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 29699 / % possible obs: 97.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 7.81 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.413 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4K1M ![]() 4k1m Resolution: 2.1→42.65 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.811 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.776 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→42.65 Å
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Refine LS restraints |
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