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- PDB-7sv4: Crystal structure of SpaA-SLH in complex with 4,6-Pyr-beta-D-ManN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sv4 | ||||||||||||
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Title | Crystal structure of SpaA-SLH in complex with 4,6-Pyr-beta-D-ManNAc-(1->4)-beta-D-GlcNAc-(1->3)-4,6-Pyr-beta-D-ManNAcOMe | ||||||||||||
![]() | Surface (S-) layer glycoprotein | ||||||||||||
![]() | 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-D4I / Surface (S-) layer glycoprotein![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Legg, M.S.G. / Evans, S.V. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.9 KB | Display | ![]() |
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PDB format | ![]() | 35.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.9 KB | Display | ![]() |
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Full document | ![]() | 797.8 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sv3C ![]() 7sv5C ![]() 7sv6C ![]() 6cwmS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19784.240 Da / Num. of mol.: 1 / Fragment: SLH domains (UNP residues 21-193) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-D4I / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.7 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Magnesium Chloride, 0.1 M Bis-Tris pH 5.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 15, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.06→20 Å / Num. obs: 11130 / % possible obs: 98.4 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.043 / Rrim(I) all: 0.15 / Χ2: 0.804 / Net I/σ(I): 13.5 / Num. measured all: 113668 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6CWM Resolution: 2.06→19.88 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.158 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.194 / 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: 66.71 Å2 / Biso mean: 23.747 Å2 / Biso min: 6.72 Å2
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Refinement step | Cycle: final / Resolution: 2.06→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.113 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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