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Yorodumi- PDB-8hic: Crystal structure of UrtA from Prochlorococcus marinus str. MIT 9... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hic | ||||||
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Title | Crystal structure of UrtA from Prochlorococcus marinus str. MIT 9313 in complex with urea and calcium | ||||||
Components | Putative urea ABC transporter, substrate binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Transporter / Complex / Urea / UrtA | ||||||
Function / homology | Urea ABC transporter, substrate-binding protein UrtA-like / Periplasmic binding protein domain / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / UREA / Putative urea ABC transporter, substrate binding protein Function and homology information | ||||||
Biological species | Prochlorococcus marinus str. MIT 9313 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Zhang, Y.Z. / Wang, P. / Wang, C. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Structural and molecular basis for urea recognition by Prochlorococcus. Authors: Wang, C. / Zhu, W.J. / Ding, H.T. / Liu, N.H. / Cao, H.Y. / Suo, C.L. / Liu, Z.K. / Zhang, Y. / Sun, M.L. / Fu, H.H. / Li, C.Y. / Chen, X.L. / Zhang, Y.Z. / Wang, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hic.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hic.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 8hic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hic_validation.pdf.gz | 727.2 KB | Display | wwPDB validaton report |
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Full document | 8hic_full_validation.pdf.gz | 727 KB | Display | |
Data in XML | 8hic_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 8hic_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/8hic ftp://data.pdbj.org/pub/pdb/validation_reports/hi/8hic | HTTPS FTP |
-Related structure data
Related structure data | 1peaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45651.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prochlorococcus marinus str. MIT 9313 (bacteria) Gene: urtA, PMT_2229 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7V3V9 | ||||
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#2: Chemical | ChemComp-URE / | ||||
#3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.16 M calcium chloride, 0.1 M sodium acetate (pH 4.8), 16% (w/v) polyethylene glycol (PEG) 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 836660 / % possible obs: 98.97 % / Redundancy: 5.1 % / Biso Wilson estimate: 11.46 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.042 / Rrim(I) all: 0.1 / Net I/σ(I): 17.99 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.426 / Num. unique obs: 836660 / CC1/2: 0.887 / Rpim(I) all: 0.196 / Rrim(I) all: 0.471 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PEA Resolution: 1.6→25.82 Å / SU ML: 0.1357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7807 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 14.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→25.82 Å
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Refine LS restraints |
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LS refinement shell |
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