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Yorodumi- PDB-7sv6: Crystal structure of SpaA-SLH/G46A/G109A in complex with 4,6-Pyr-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sv6 | ||||||||||||
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Title | Crystal structure of SpaA-SLH/G46A/G109A in complex with 4,6-Pyr-beta-D-ManNAc-(1->4)-beta-D-GlcNAcOMe | ||||||||||||
Components | Surface (S-) layer glycoprotein | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / S-layer / SLH domain / Secondary cell wall polymer | ||||||||||||
Function / homology | S-layer homology domain / S-layer homology (SLH) domain profile. / Copper resistance protein CopC/internalin, immunoglobulin-like / Chem-D2Y / Surface (S-) layer glycoprotein Function and homology information | ||||||||||||
Biological species | Paenibacillus alvei (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||||||||
Authors | Legg, M.S.G. / Evans, S.V. | ||||||||||||
Funding support | Austria, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: The S-layer homology domains of Paenibacillus alvei surface protein SpaA bind to cell wall polysaccharide through the terminal monosaccharide residue. Authors: Legg, M.S.G. / Hager-Mair, F.F. / Krauter, S. / Gagnon, S.M.L. / Lopez-Guzman, A. / Lim, C. / Blaukopf, M. / Kosma, 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 | 7sv6.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sv6.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 7sv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/7sv6 ftp://data.pdbj.org/pub/pdb/validation_reports/sv/7sv6 | HTTPS FTP |
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-Related structure data
Related structure data | 7sv3C 7sv4C 7sv5C 6cwmS C: citing same article (ref.) S: Starting model for refinement |
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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1JZ07 |
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#2: Chemical | ChemComp-D2Y / |
#3: 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: 1.99 Å3/Da / Density % sol: 38.29 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate, 25% (w/v) PEG 4000, 8% (w/v) isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 25, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→20 Å / Num. obs: 13823 / % possible obs: 98.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.053 / Rrim(I) all: 0.113 / Χ2: 0.962 / Net I/σ(I): 8.1 / Num. measured all: 59023 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CWM Resolution: 1.85→19.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.249 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.52 Å2 / Biso mean: 21.533 Å2 / Biso min: 13.49 Å2
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Refinement step | Cycle: final / Resolution: 1.85→19.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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