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Yorodumi- PDB-3b9z: Crystal structure of the Nitrosomonas europaea Rh protein complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b9z | ||||||
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Title | Crystal structure of the Nitrosomonas europaea Rh protein complexed with carbon dioxide | ||||||
Components | Ammonium transporter family Rh-like protein | ||||||
Keywords | TRANSPORT PROTEIN / carbon dioxide / channel / Rh protein / CO2 | ||||||
Function / homology | Function and homology information ammonium transmembrane transporter activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Nitrosomonas europaea ATCC 19718 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Li, X. / Jayachandran, S. / Nguyen, H.-H.T. / Chan, M.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Structure of the Nitrosomonas europaea Rh protein. Authors: Li, X. / Jayachandran, S. / Nguyen, H.H. / Chan, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b9z.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b9z.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 3b9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/3b9z ftp://data.pdbj.org/pub/pdb/validation_reports/b9/3b9z | HTTPS FTP |
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-Related structure data
Related structure data | 3b9ySC 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 40783.473 Da / Num. of mol.: 1 / Fragment: Residues 31-418 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria) Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: Rh50, NE0448 / Production host: Methylococcus capsulatus (bacteria) / References: UniProt: Q82X47 | ||||||
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#2: Sugar | #3: Chemical | ChemComp-CO2 / | #4: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #5: 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: 3.41 Å3/Da / Density % sol: 63.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 14.5% PEG 2000 MME, 1 mM EDTA, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.91837 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91837 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→41.631 Å / Num. all: 46080 / Num. obs: 45094 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 17.744 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 7.48 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3309 / Rsym value: 0.425 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3B9Y Resolution: 1.85→41.631 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.845 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.102 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→41.631 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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