+Open data
-Basic information
Entry | Database: PDB / ID: 4ayz | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | X-ray Structure of human SOUL | |||||||||
Components | (HEME-BINDING PROTEIN 2) x 2 | |||||||||
Keywords | APOPTOSIS / HEME BINDING PROTEIN | |||||||||
Function / homology | Function and homology information azurophil granule lumen / heme binding / Neutrophil degranulation / mitochondrion / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å | |||||||||
Authors | Freire, F. / Carvalho, A.L. / Aveiro, S.S. / Charbonnier, P. / Moulis, J.M. / Romao, M.J. / Goodfellow, B.J. / Macedo, A.L. | |||||||||
Citation | Journal: To be Published Title: Human Soul: A Heme-Binding or a Bh3 Domain-Containing Protein Authors: Freire, F. / Carvalho, A.L. / Aveiro, S.S. / Charbonnier, P. / Moulis, J.M. / Romao, M.J. / Goodfellow, B.J. / Macedo, A.L. | |||||||||
History |
| |||||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ayz.cif.gz | 147.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ayz.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ayz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/4ayz ftp://data.pdbj.org/pub/pdb/validation_reports/ay/4ayz | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 23396.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9Y5Z4 |
---|---|
#2: Protein | Mass: 23396.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9Y5Z4 |
Sequence details | ALA MET HIS RESIDUES IN N-TERMINAL ARE FROM THE EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72 % / Description: NONE |
---|---|
Crystal grow | pH: 5.6 / Details: 1.8 M NA/K PHOSPHATE BUFFER 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 11094 / % possible obs: 100 % / Observed criterion σ(I): 4.1 / Redundancy: 13.6 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 11 |
Reflection shell | Resolution: 3.5→3.69 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 3.5→50 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.854 / SU B: 56.814 / SU ML: 0.395 / Cross valid method: THROUGHOUT / ESU R: 1.071 / ESU R Free: 0.516 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.35 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|