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Yorodumi- PDB-6ixi: structure of Cd-bound periplasmic metal binding protein from cand... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ixi | ||||||
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Title | structure of Cd-bound periplasmic metal binding protein from candidatus liberibacter asiaticus | ||||||
Components | Periplasmic solute binding protein | ||||||
Keywords | METAL BINDING PROTEIN / Candidatus Liberibacter asiaticus / Periplasmic | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Candidatus Liberibacter asiaticus str. psy62 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Kumar, P. / Sharma, N. / Dalal, V. / Ghosh, D.K. / Kumar, P. / Sharma, A.K. | ||||||
Citation | Journal: Metallomics / Year: 2020 Title: Characterization of the heavy metal binding properties of periplasmic metal uptake protein CLas-ZnuA2. Authors: Kumar, P. / Dalal, V. / Sharma, N. / Kokane, S. / Ghosh, D.K. / Kumar, P. / Sharma, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ixi.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ixi.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ixi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ixi_validation.pdf.gz | 471.1 KB | Display | wwPDB validaton report |
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Full document | 6ixi_full_validation.pdf.gz | 475.4 KB | Display | |
Data in XML | 6ixi_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 6ixi_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/6ixi ftp://data.pdbj.org/pub/pdb/validation_reports/ix/6ixi | HTTPS FTP |
-Related structure data
Related structure data | 4cl2S S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30897.055 Da / Num. of mol.: 1 / Fragment: UNP residues 20-294 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Liberibacter asiaticus str. psy62 (bacteria) Gene: CLIBASIA_02120 / Details (production host): pET28c / Production host: Escherichia coli (E. coli) / References: UniProt: C6XF58 |
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-Non-polymers , 5 types, 228 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-ACT / #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: 3.82 Å3/Da / Density % sol: 67 % / Description: Cubic |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2M ammonium sulphate, 0.1M Sodium acetate Trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 29875 / % possible obs: 96.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 39.4 Å2 / CC1/2: 1 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.06→2.1 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 664 / CC1/2: 0.52 / % possible all: 53.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CL2 Resolution: 2.07→46.68 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.645 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.139 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.564 Å2
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Refinement step | Cycle: 1 / Resolution: 2.07→46.68 Å
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Refine LS restraints |
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