+Open data
-Basic information
Entry | Database: PDB / ID: 8jv2 | ||||||
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Title | Structure of the SAR11 PotD in complex with proline | ||||||
Components | Spermidine/putrescine-binding periplasmic protein | ||||||
Keywords | TRANSPORT PROTEIN / PotD / substrate binding protein / solute-binding protein / periplasmic binding protein / ABC transporter system receptor / osmolyte / compatible solute / betaine / DMSP / GABA / amino acid / SAR11 / Candidatus Pelagibacter sp. HTCC7211 | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / PROLINE / Spermidine/putrescine-binding periplasmic protein Function and homology information | ||||||
Biological species | Pelagibacter sp. | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Ma, Q. / Liu, C. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of the SAR11 PotD in complex with proline Authors: Ma, Q. / Liu, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jv2.cif.gz | 173.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jv2.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 8jv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jv2_validation.pdf.gz | 750.3 KB | Display | wwPDB validaton report |
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Full document | 8jv2_full_validation.pdf.gz | 750.5 KB | Display | |
Data in XML | 8jv2_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 8jv2_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/8jv2 ftp://data.pdbj.org/pub/pdb/validation_reports/jv/8jv2 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39442.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pelagibacter sp. (strain HTCC7211) (bacteria) Gene: potD, PB7211_697 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: B6BQH5 |
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-Non-polymers , 5 types, 440 molecules
#2: Chemical | ChemComp-PRO / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.75 Å3/Da / Density % sol: 55.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: The protein in complex with L-proline was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, 50 mM L-proline, pH 7.5) and ...Details: The protein in complex with L-proline was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, 50 mM L-proline, pH 7.5) and 1 ul reservoir solution (100 mM MES pH 6.5, 20% w/v mPEG 550). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→55.733 Å / Num. obs: 104876 / % possible obs: 97.7 % / Redundancy: 12.4 % / CC1/2: 1 / Rpim(I) all: 0.011 / Rrim(I) all: 0.041 / Rsym value: 0.039 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 1.3→1.322 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4306 / CC1/2: 0.874 / Rpim(I) all: 0.157 / Rrim(I) all: 0.457 / Rsym value: 0.426 / % possible all: 81 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→26.235 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 10.75 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→26.235 Å
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Refine LS restraints |
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LS refinement shell |
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