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Yorodumi- PDB-4ry1: Crystal structure of periplasmic solute binding protein ECA2210 f... -
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-Basic information
Entry | Database: PDB / ID: 4ry1 | ||||||
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Title | Crystal structure of periplasmic solute binding protein ECA2210 from Pectobacterium atrosepticum SCRI1043, Target EFI-510858 | ||||||
Components | Periplasmic solute binding protein | ||||||
Keywords | TRANSPORT PROTEIN / SUGAR TRANSPORTER / ABC-TYPE / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / Periplasmic binding protein Function and homology information | ||||||
Biological species | Pectobacterium atrosepticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Hillerich, B. / Siedel, R.D. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of periplasmic solute binding protein ECA2210 from Pectobacterium atrosepticum, Target EFI-510858 Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Hillerich, B. / Morisco, L.L. / Wasserman, S.R. / ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Hillerich, B. / Morisco, L.L. / Wasserman, S.R. / Siedel, R.D. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ry1.cif.gz | 376.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ry1.ent.gz | 308.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ry1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/4ry1 ftp://data.pdbj.org/pub/pdb/validation_reports/ry/4ry1 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 45616.703 Da / Num. of mol.: 2 / Fragment: UNP residues 31-439 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Strain: SCRI 1043 / ATCC BAA-672 / Gene: ECA2210 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6D532 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.28 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT); RESERVOIR: 0.085 M TRIS-HCL, PH 8.5, 0.17 M SODIUM ACETATE, 25% PEG3350, 15% (V/V) GLYCEROL; CRYOPROTECTION: RESERVOIR SOLUTION, VAPOR DIFFUSION, ...Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT); RESERVOIR: 0.085 M TRIS-HCL, PH 8.5, 0.17 M SODIUM ACETATE, 25% PEG3350, 15% (V/V) GLYCEROL; CRYOPROTECTION: RESERVOIR SOLUTION, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 5, 2014 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 160376 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.172 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.053 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→50 Å
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