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Yorodumi- PDB-6mm2: Carbon regulatory PII-like protein SbtB from Cyanobium sp. 7001 b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mm2 | ||||||
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Title | Carbon regulatory PII-like protein SbtB from Cyanobium sp. 7001 bound to ATP and calcium | ||||||
Components | Carbon regulatory PII-like protein SbtB | ||||||
Keywords | SIGNALING PROTEIN / PII-like protein / SbtB / regulatory protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cyanobium sp. PCC 7001 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | ||||||
Authors | Kaczmarski, J.A. / Jackson, C. | ||||||
Citation | Journal: Biorxiv / Year: 2019 Title: Structure and function of SbtB from Cyanobium sp. 7001 Authors: Jackson, C. / Kaczmarski, J.A. / Price, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mm2.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mm2.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 6mm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mm2_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6mm2_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6mm2_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 6mm2_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/6mm2 ftp://data.pdbj.org/pub/pdb/validation_reports/mm/6mm2 | HTTPS FTP |
-Related structure data
Related structure data | 6mmcC 6mmoC 6mmqC 6n4aC 6ntbC 5o3pS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11484.044 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanobium sp. PCC 7001 (bacteria) / Gene: CPCC7001_1671 / Plasmid: pETMCSIII / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5II98 |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30 % 2-methyl-2,4-pentanediol 0.02 M calcium chloride 0.1 M sodium acetate-acetic acid pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→16.045 Å / Num. obs: 44144 / % possible obs: 95.3 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.02 / Rrim(I) all: 0.043 / Χ2: 0.87 / Net I/av σ(I): 21.8 / Net I/σ(I): 0.999 |
Reflection shell | Resolution: 1.04→1.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.337 / Num. unique obs: 2573 / CC1/2: 0.405 / % possible all: 50.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5O3P Resolution: 1.04→16.04 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.04→16.04 Å
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LS refinement shell | Resolution: 1.04→1.076 Å
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