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Yorodumi- PDB-6cwr: Crystal structure of SpaA-SLH/G46A/G109A in complex with 4,6-Pyr-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cwr | ||||||||||||
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Title | Crystal structure of SpaA-SLH/G46A/G109A in complex with 4,6-Pyr-beta-D-ManNAcOMe | ||||||||||||
Components | Surface (S-) layer glycoprotein | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / Surface layer homology domain / Secondary cell wall polymer / S-layer / SLH / SCWP | ||||||||||||
Function / homology | S-layer homology domain / S-layer homology (SLH) domain profile. / Copper resistance protein CopC/internalin, immunoglobulin-like / Chem-6LA / Surface (S-) layer glycoprotein Function and homology information | ||||||||||||
Biological species | Paenibacillus alvei (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||||||||
Authors | Blackler, R.J. / Gagnon, S.M.L. / Haji-Ghassemi, O. / Evans, S.V. | ||||||||||||
Funding support | Canada, Austria, 3items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis of cell wall anchoring by SLH domains in Paenibacillus alvei. Authors: Blackler, R.J. / Lopez-Guzman, A. / Hager, F.F. / Janesch, B. / Martinz, G. / Gagnon, S.M.L. / Haji-Ghassemi, O. / Kosma, P. / Messner, P. / Schaffer, C. / Evans, S.V. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cwr.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cwr.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 6cwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/6cwr ftp://data.pdbj.org/pub/pdb/validation_reports/cw/6cwr | HTTPS FTP |
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-Related structure data
Related structure data | 6cwcSC 6cwfC 6cwhC 6cwiC 6cwlC 6cwmC 6cwnC 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
#1: Protein | Mass: 19812.291 Da / Num. of mol.: 1 / Fragment: SLH domains (UNP residues 21-193) / Mutation: G46A, G109A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus alvei (bacteria) / Gene: spaA / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1JZ07 |
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#2: Sugar | ChemComp-6LA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 36.74 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris, pH 6.5, 28% PEG2000 MME |
-Data collection
Diffraction | Mean temperature: 289 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.24→30 Å / Num. obs: 44339 / % possible obs: 99.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.02 / Rrim(I) all: 0.045 / Χ2: 1.006 / Net I/av σ(I): 27.238 / Net I/σ(I): 16.1 / Num. measured all: 181698 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6CWC Resolution: 1.24→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.679 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.042 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.47 Å2 / Biso mean: 18.404 Å2 / Biso min: 9.58 Å2
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Refinement step | Cycle: final / Resolution: 1.24→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.239→1.271 Å / Total num. of bins used: 20
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