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Yorodumi- PDB-7s6e: Crystal structure of UrtA from Synechococcus CC9311 in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s6e | |||||||||
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Title | Crystal structure of UrtA from Synechococcus CC9311 in complex with urea and calcium | |||||||||
Components | Urea ABC transporter, periplasmic urea-binding protein | |||||||||
Keywords | TRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / urea-binding protein | |||||||||
Function / homology | Urea ABC transporter, substrate-binding protein UrtA-like / Periplasmic binding protein-like I / UREA / Urea ABC transporter, periplasmic urea-binding protein Function and homology information | |||||||||
Biological species | Synechococcus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.973 Å | |||||||||
Authors | Shah, B.S. / Mikolajek, H. / Mykhaylyk, V. / Orr, C.M. / Owens, R.J. / Paulsen, I.T. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: To Be Published Title: Crystal structure of UrtA from Synechococcus CC9311 in complex with urea and calcium Authors: Shah, B.S. / Mikolajek, H. / Mykhaylyk, V. / Orr, C.M. / Owens, R. / Paulsen, I.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s6e.cif.gz | 323.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s6e.ent.gz | 263.7 KB | Display | PDB format |
PDBx/mmJSON format | 7s6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/7s6e ftp://data.pdbj.org/pub/pdb/validation_reports/s6/7s6e | HTTPS FTP |
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-Related structure data
Similar structure data |
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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, 2 molecules AB
#1: Protein | Mass: 44223.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. (strain CC9311) (bacteria) Strain: CC9311 / Gene: sync_2872 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: Q0I663 |
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-Non-polymers , 5 types, 662 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-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: 2.01 Å3/Da / Density % sol: 38.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.062 M MES; 0.038 imidazole, pH 6.5, 0.03M MgCl2, 0.03M CaCl2.2H2O, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD |
-Data collection
Diffraction | Mean temperature: 50 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.0240, 3.3509, 4.2753, 4.7686 | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jun 26, 2020 | |||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.97→85.114 Å / Num. obs: 49942 / % possible obs: 93.3 % / Redundancy: 15.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.026 / Rrim(I) all: 0.08 / Net I/σ(I): 22.8 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.973→85.114 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.168 / WRfactor Rwork: 0.146 / SU B: 2.842 / SU ML: 0.08 / Average fsc free: 0.9627 / Average fsc work: 0.969 / Cross valid method: FREE R-VALUE / ESU R: 0.177 / ESU R Free: 0.135 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.602 Å2
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Refinement step | Cycle: LAST / Resolution: 1.973→85.114 Å
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Refine LS restraints |
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LS refinement shell |
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