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Yorodumi- PDB-2g29: crystal structure of the periplasmic nitrate-binding protein NrtA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g29 | ||||||
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Title | crystal structure of the periplasmic nitrate-binding protein NrtA from Synechocystis PCC 6803 | ||||||
Components | Nitrate transport protein nrtA | ||||||
Keywords | TRANSPORT PROTEIN / solute-binding protein / alpha-beta protein | ||||||
Function / homology | Function and homology information transmembrane transporter activity / nitrate assimilation / monoatomic ion transport / plasma membrane Similarity search - Function | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Koropatkin, N.M. / Pakrasi, H.B. / Smith, T.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Atomic structure of a nitrate-binding protein crucial for photosynthetic productivity Authors: Koropatkin, N.M. / Pakrasi, H.B. / Smith, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g29.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g29.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 2g29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g29_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
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Full document | 2g29_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 2g29_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 2g29_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/2g29 ftp://data.pdbj.org/pub/pdb/validation_reports/g2/2g29 | HTTPS FTP |
-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
#1: Protein | Mass: 45952.785 Da / Num. of mol.: 1 / Fragment: solute-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Gene: nrtA / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P73452 |
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#2: Chemical | ChemComp-NO3 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M succinate, 20 mM sodium nitrate, 2.0-2.2M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97899, 0.97915, 0.97132 | ||||||||||||
Detector | Type: SBC-3 / Detector: CCD / Date: Nov 3, 2005 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→50 Å / Num. all: 57966 / Num. obs: 57966 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.059 / Net I/σ(I): 20.3 | ||||||||||||
Reflection shell | Resolution: 1.5→1.56 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 6 / Rsym value: 0.15 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.56 Å /
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