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Yorodumi- PDB-3nd0: X-ray crystal structure of a slow cyanobacterial Cl-/H+ antiporter -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nd0 | ||||||
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Title | X-ray crystal structure of a slow cyanobacterial Cl-/H+ antiporter | ||||||
Components | Sll0855 protein | ||||||
Keywords | TRANSPORT PROTEIN / CLC family CL-/H+ antiporter / CLC_EC1 homolog / Synechocystis sp. PCC 6803 / P73745 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Synechocystis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å | ||||||
Authors | Jayaram, H. / Robertson, J. / Wu, F. / Williams, C. / Miller, C. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Structure of a Slow CLC Cl(-)/H(+) Antiporter from a Cyanobacterium. Authors: Jayaram, H. / Robertson, J.L. / Wu, F. / Williams, C. / Miller, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nd0.cif.gz | 166.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nd0.ent.gz | 133.4 KB | Display | PDB format |
PDBx/mmJSON format | 3nd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/3nd0 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/3nd0 | HTTPS FTP |
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-Related 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 domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 50105.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis (bacteria) / Strain: PCC 6803 / Gene: sll0855 / Plasmid details: 469008 / Plasmid: pASK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P73745 #2: Chemical | |
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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: 5.8 Å3/Da / Density % sol: 80.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30 % PEG 400, 200 mM CaCl2 , Tris-HCl 100 mM pH 8, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 78 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→67 Å / Num. all: 35234 / Num. obs: 35234 / % possible obs: 92 % / Redundancy: 15.1 % / Rsym value: 0.258 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 31.69 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→65.219 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.865 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.52 / σ(F): 0.16 / Phase error: 25.15 / Stereochemistry target values: ML / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.135 Å2 / ksol: 0.272 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.2→65.219 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3195 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell |
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