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Yorodumi- PDB-9dsy: Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein... -
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-Basic information
Entry | Database: PDB / ID: 9dsy | ||||||
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Title | Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Succinic Acid | ||||||
Components | C4-dicarboxylate-binding periplasmic protein DctP | ||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / DctP / Succinic acid / Center for Structural Biology of Infectious Diseases / CSBID | ||||||
Function / homology | C4-dicarboxylate transport / TRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / SUCCINIC ACID / C4-dicarboxylate-binding periplasmic protein DctP Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Minasov, G. / Shukla, S. / Shuvalova, L. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Succinic Acid Authors: Minasov, G. / Shukla, S. / Shuvalova, L. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9dsy.cif.gz | 151.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9dsy.ent.gz | 118 KB | Display | PDB format |
PDBx/mmJSON format | 9dsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9dsy_validation.pdf.gz | 725.7 KB | Display | wwPDB validaton report |
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Full document | 9dsy_full_validation.pdf.gz | 729.6 KB | Display | |
Data in XML | 9dsy_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 9dsy_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/9dsy ftp://data.pdbj.org/pub/pdb/validation_reports/ds/9dsy | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35423.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: dctP, PA5167 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9HU18 | ||||||
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#2: Chemical | ChemComp-SIN / | ||||||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.7 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: Protein: 7.0 mg/ml, 0.5M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM Succinic acid; Screen: Classics II (H9), 0.05M Zing acetate, 20% (w/v) PEG 3350; Cryo: Reservoir. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2022 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. obs: 55717 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 13.7 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.063 / Rrim(I) all: 0.121 / Rsym value: 0.103 / Χ2: 1.01 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2681 / CC1/2: 0.559 / CC star: 0.847 / Rpim(I) all: 0.894 / Χ2: 0.994 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→29.85 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.409 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.062 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.752 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→29.85 Å
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