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Yorodumi- PDB-8a0c: Capsular polysaccharide synthesis multienzyme in complex with CMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a0c | ||||||||||||
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Title | Capsular polysaccharide synthesis multienzyme in complex with CMP | ||||||||||||
Components | Bcs3 | ||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / Bacterial capsule synthesis | ||||||||||||
Function / homology | Function and homology information CDP-glycerol glycerophosphotransferase activity / teichoic acid biosynthetic process / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||||||||
Authors | Cifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon-Roth, I. / Berger, M. ...Cifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon-Roth, I. / Berger, M. / Claus, H. / DAngelo, C. / Marina, A. / Gerardy-Schahn, R. / Schubert, M. / Guerin, M.E. / Fiebig, T. | ||||||||||||
Funding support | Germany, Spain, United States, 3items
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Citation | Journal: Nat.Chem.Biol. / Year: 2023 Title: A multi-enzyme machine polymerizes the Haemophilus influenzae type b capsule. Authors: Cifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon Roth, I. / Berger, M. / Claus, H. / D'Angelo, C. / Marina, A. / ...Authors: Cifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon Roth, I. / Berger, M. / Claus, H. / D'Angelo, C. / Marina, A. / Gerardy-Schahn, R. / Schubert, M. / Guerin, M.E. / Fiebig, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a0c.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8a0c.ent.gz | 713 KB | Display | PDB format |
PDBx/mmJSON format | 8a0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a0c_validation.pdf.gz | 780.6 KB | Display | wwPDB validaton report |
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Full document | 8a0c_full_validation.pdf.gz | 798.7 KB | Display | |
Data in XML | 8a0c_validation.xml.gz | 77.8 KB | Display | |
Data in CIF | 8a0c_validation.cif.gz | 107.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/8a0c ftp://data.pdbj.org/pub/pdb/validation_reports/a0/8a0c | HTTPS FTP |
-Related structure data
Related structure data | 8a0mC C: citing same article (ref.) |
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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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 137535.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: bcs3', bcs3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2ERG0 |
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-Non-polymers , 5 types, 458 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-C5P / | #6: Water | ChemComp-HOH / | |
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-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: 3.19 Å3/Da / Density % sol: 61.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.04 M Potassium phosphate monobasic None 16 % w/v PEG 8000 20 % v/v Glycerol 5mM CMP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→302.57 Å / Num. obs: 75365 / % possible obs: 99.9 % / Redundancy: 19.1 % / Biso Wilson estimate: 43.94 Å2 / CC1/2: 1 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 2.39→2.43 Å / Num. unique obs: 6517 / CC1/2: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Alphafold Resolution: 2.9→57.4 Å / SU ML: 0.3625 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8894 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 43.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→57.4 Å
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Refine LS restraints |
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LS refinement shell |
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