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Yorodumi- PDB-3csx: Structural characterization of a protein in the DUF683 family- cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3csx | ||||||
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Title | Structural characterization of a protein in the DUF683 family- crystal structure of cce_0567 from the cyanobacterium Cyanothece 51142. | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | METAL BINDING PROTEIN / UNKNOWN FUNCTION / metalloprotein / nitrogen fixation / cyanobacteria / circadian rhythms | ||||||
Function / homology | Putative nitrogen fixation protein / Rop-like / Helix hairpin bin / Helix hairpin bin domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / NICKEL (II) ION / DUF683-containing protein Function and homology information | ||||||
Biological species | Cyanothece (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å | ||||||
Authors | Addlagatta, A. / Robinson, H. / Buchko, G.W. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2009 Title: Structural characterization of the protein cce_0567 from Cyanothece 51142, a metalloprotein associated with nitrogen fixation in the DUF683 family. Authors: Buchko, G.W. / Robinson, H. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3csx.cif.gz | 41.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3csx.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 3csx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/3csx ftp://data.pdbj.org/pub/pdb/validation_reports/cs/3csx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9287.580 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanothece (bacteria) / Strain: ATCC 51142 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1KYE3 #2: Chemical | ChemComp-NI / | #3: 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: 1.89 Å3/Da / Density % sol: 34.99 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 2 uL Protein (~2 mg/mL protein in 500 mM NaCl, 20 mM TrisHCl, 1.0 mM DTT, pH 7.2) plus 2 uL Precipatant (30% w/v PEG 1500, 1 mM NiCl2)., VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97935 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→30 Å / Num. all: 11230 / Num. obs: 11230 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.84→1.92 Å / % possible all: 52 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.84→29.24 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.894 / SU B: 3.359 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.18 / ESU R Free: 0.183 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.145 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→29.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.887 Å / Total num. of bins used: 20
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