+Open data
-Basic information
Entry | Database: PDB / ID: 7psq | ||||||
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Title | Crystal structure of S100A4 labeled with NU074381b. | ||||||
Components | Protein S100-A4 | ||||||
Keywords | CYTOSOLIC PROTEIN / Covalent inhibitor / Protein labeling / calcium-binding protein / S100-protein family. | ||||||
Function / homology | Function and homology information RAGE receptor binding / chemoattractant activity / transition metal ion binding / epithelial to mesenchymal transition / calcium-dependent protein binding / actin binding / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / calcium ion binding / perinuclear region of cytoplasm ...RAGE receptor binding / chemoattractant activity / transition metal ion binding / epithelial to mesenchymal transition / calcium-dependent protein binding / actin binding / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / calcium ion binding / perinuclear region of cytoplasm / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Giroud, C. / Szommer, T. / Coxon, C. / Monteiro, O. / Christott, T. / Bennett, J. / Aitmakhanova, K. / Raux, B. / Newman, J. / Elkins, J. ...Giroud, C. / Szommer, T. / Coxon, C. / Monteiro, O. / Christott, T. / Bennett, J. / Aitmakhanova, K. / Raux, B. / Newman, J. / Elkins, J. / Krojer, T. / Arruda Bezerra, G. / Koekemoer, L. / Bountra, C. / Von Delft, F. / Brennan, P. / Fedorov, O. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: Crystal structure of S100A4 labeled with NU074381b. Authors: Giroud, C. / Szommer, T. / Coxon, C. / Monteiro, O. / Christott, T. / Bennett, J. / Aitmakhanova, K. / Raux, B. / Newman, J. / Elkins, J. / Krojer, T. / Koekemoer, L. / Von Delft, F. / ...Authors: Giroud, C. / Szommer, T. / Coxon, C. / Monteiro, O. / Christott, T. / Bennett, J. / Aitmakhanova, K. / Raux, B. / Newman, J. / Elkins, J. / Krojer, T. / Koekemoer, L. / Von Delft, F. / Bountr, C. / Brennan, P. / Fedorov, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7psq.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7psq.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 7psq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7psq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7psq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7psq_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 7psq_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/7psq ftp://data.pdbj.org/pub/pdb/validation_reports/ps/7psq | HTTPS FTP |
-Related structure data
Related structure data | 3c1vS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14313.247 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: S100A4, CAPL, MTS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26447 #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MES 25mM, 12.5% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→43.63 Å / Num. obs: 34616 / % possible obs: 99 % / Redundancy: 13.4 % / Biso Wilson estimate: 49.23 Å2 / CC1/2: 1 / Χ2: 0.99 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 8.9→42.77 Å / Num. unique obs: 461 / CC1/2: 0.999 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C1V Resolution: 1.91→64.91 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.89 / Stereochemistry target values: ML
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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 max: 127.63 Å2 / Biso mean: 59.0107 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.91→64.91 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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