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- PDB-4p3l: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4p3l | ||||||
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Title | CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM CHROMOHALOBACTER SALEXIGENS DSM 3043 (Csal_2479), TARGET EFI-510085, WITH BOUND GLUCURONATE, SPG P6122 | ||||||
![]() | TRAP dicarboxylate transporter, DctP subunit | ||||||
![]() | SOLUTE-BINDING PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics | ||||||
Function / homology | ![]() carbohydrate transport / transmembrane transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.9 KB | Display | ![]() |
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PDB format | ![]() | 154.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.1 KB | Display | ![]() |
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Full document | ![]() | 436.1 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ln5C ![]() 4mcoC ![]() 4mevC ![]() 4mhfC ![]() 4mijC ![]() 4mncC ![]() 4mniC ![]() 4mx6C ![]() 4n15C ![]() 4n17C ![]() 4n4uC ![]() 4n6dC ![]() 4n6kC ![]() 4n8gC ![]() 4n8yC ![]() 4n91C ![]() 4napC ![]() 4nf0C ![]() 4ng7C ![]() 4nguC ![]() 4nhbC ![]() 4nn3C ![]() 4nq8C ![]() 4nx1C ![]() 4o7mC ![]() 4o8mC ![]() 4o94C ![]() 4oa4C ![]() 4oanC ![]() 4ovpC ![]() 4ovqC ![]() 4ovrC ![]() 4ovsC ![]() 4ovtC ![]() 4p1eC ![]() 4p1lC ![]() 4p47C ![]() 4p56C ![]() 4p8bC ![]() 4p9kC ![]() 4pafC ![]() 4paiC ![]() 4pakC ![]() 4pbhC ![]() 4pbqC ![]() 4pc9C ![]() 4pcdC ![]() 4pddC ![]() 4pdhC ![]() 4pe3C ![]() 4petC ![]() 4pf6C ![]() 4pf8C ![]() 4pfbC ![]() 4pfiC ![]() 4pfrC ![]() 4pgnC ![]() 4pgpC ![]() 4uabC C: citing same article ( |
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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: 36996.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Sugar | ChemComp-BDP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: Protein (35.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM Glucuronate); Reservoir (0.2 M Sodium chloride, 0.1 M Phosphate-citrate, pH 4.2, 20 %(w/v) PEG 8000); Cryoprotection (20% glycerol, 80% reservoir) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Mar 1, 2014 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→80.33 Å / Num. obs: 40251 / % possible obs: 97.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.18 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.046 / Net I/σ(I): 12.3 / Num. measured all: 307566 / Scaling rejects: 34 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 6 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.4 / Num. measured all: 14421 / Num. unique all: 2408 / Rpim(I) all: 0.344 / Rejects: 0 / % possible all: 99.8 |
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Processing
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Refinement | Resolution: 1.8→47.086 Å / FOM work R set: 0.916 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.48 / Stereochemistry target values: ML
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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 max: 71.75 Å2 / Biso mean: 23.13 Å2 / Biso min: 5.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→47.086 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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