+Open data
-Basic information
Entry | Database: PDB / ID: 6st5 | ||||||
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Title | crystal structure of LicM2 | ||||||
Components | LicM2 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / crystal / ATP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.82 Å | ||||||
Authors | Gonsior, M. / Mainz, A. / Hugelland, M. / Kuthning, A. / Tietzmann, M. / Dobbek, H. / Martins, B.M. / Sussmuth, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: crystal structure of LicM2 Authors: Gonsior, M. / Martins, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6st5.cif.gz | 352.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6st5.ent.gz | 291.1 KB | Display | PDB format |
PDBx/mmJSON format | 6st5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6st5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6st5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6st5_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 6st5_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/6st5 ftp://data.pdbj.org/pub/pdb/validation_reports/st/6st5 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 111230.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: licM2 / Production host: Escherichia coli (E. coli) / References: UniProt: E9MWH4 |
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-Non-polymers , 5 types, 12 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-ANP / | ||||
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
-Details
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: 3 Å3/Da / Density % sol: 56 % / Description: long pencil-shaped |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M MgCl2, 0.1 M MOPS, 12% PEG 8000 / Temp details: incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979568 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979568 Å / Relative weight: 1 |
Reflection | Resolution: 2.817→47.503 Å / Num. obs: 35085 / % possible obs: 99.7 % / Redundancy: 13 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.96 |
Reflection shell | Resolution: 2.82→2.92 Å / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 3435 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.82→47.5 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 32.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 239.41 Å2 / Biso mean: 90 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.82→47.5 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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