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Yorodumi- PDB-4jre: Crystal structure of nitrate/nitrite exchanger NarK with nitrite bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jre | ||||||
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Title | Crystal structure of nitrate/nitrite exchanger NarK with nitrite bound | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/Immune System / Transporter / Immunoglobulin / Major Facilitator Superfamily / Exchanger / TRANSPORT PROTEIN-Immune System complex | ||||||
Function / homology | Function and homology information nitrite transmembrane transporter activity / nitrate transmembrane transport / nitrite transport / nitrate transmembrane transporter activity / nitrate catabolic process / solute:inorganic anion antiporter activity / nitrate assimilation / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Zheng, H. / Wisedchaisri, G. / Gonen, T. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Crystal structure of a nitrate/nitrite exchanger. Authors: Zheng, H. / Wisedchaisri, G. / Gonen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jre.cif.gz | 323.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jre.ent.gz | 257.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jre_validation.pdf.gz | 503.5 KB | Display | wwPDB validaton report |
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Full document | 4jre_full_validation.pdf.gz | 543.1 KB | Display | |
Data in XML | 4jre_validation.xml.gz | 58.4 KB | Display | |
Data in CIF | 4jre_validation.cif.gz | 79.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/4jre ftp://data.pdbj.org/pub/pdb/validation_reports/jr/4jre | HTTPS FTP |
-Related structure data
Related structure data | 4jr9SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Antibody , 2 types, 4 molecules BHCL
#2: Antibody | Mass: 23188.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma #3: Antibody | Mass: 23265.705 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma |
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-Protein / Sugars , 2 types, 4 molecules AD
#1: Protein | Mass: 50009.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1223, JW1214, narK / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) C41 / References: UniProt: P10903 #5: Sugar | |
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-Non-polymers , 2 types, 37 molecules
#4: Chemical | #6: Water | ChemComp-HOH / | |
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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: 4.14 Å3/Da / Density % sol: 70.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 28% PEG400, 0.1 M citric acid pH 3.5, 0.1M NaCl and 0.1M Li2SO4. The crystal was subsequently soaked with 50mM NaNO2 in the above solution prior to freezing, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99999 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2012 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 72283 / % possible obs: 94.6 % / Observed criterion σ(I): 1.1 / Redundancy: 3.6 % / Biso Wilson estimate: 57.7 Å2 / Rsym value: 0.158 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 2893 / Rsym value: 0.866 / % possible all: 76.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4JR9 Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.859 / SU B: 12.544 / SU ML: 0.247 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: A strong density on the surface of NarK is likely from the sugar head group of the decylmaltoside detergent used during protein purification and is modelled in the structure as maltose.
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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: 57.172 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3741 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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