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- PDB-5zha: Structure of Y68F mutant Mn-Bound periplasmic metal binding prote... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zha | ||||||
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Title | Structure of Y68F mutant Mn-Bound periplasmic metal binding protein from candidatus liberibacter asiaticus | ||||||
![]() | Periplasmic solute binding protein | ||||||
![]() | METAL BINDING PROTEIN / ABC transporter / Periplasmic metal binding protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Saini, G. / Sharma, N. / Dalal, V. / Kumar, P. / Sharma, A.K. | ||||||
![]() | ![]() Title: The analysis of subtle internal communications through mutation studies in periplasmic metal uptake protein CLas-ZnuA2 Authors: Saini, G. / Sharma, N. / Dalal, V. / Warghane, A. / Ghosh, D.K. / Kumar, P. / Sharma, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146 KB | Display | ![]() |
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PDB format | ![]() | 113.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.2 KB | Display | ![]() |
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Full document | ![]() | 475.3 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5z2jC ![]() 5z2kC ![]() 5z35C ![]() 4udnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30881.055 Da / Num. of mol.: 1 / Fragment: UNP residues 20-294 / Mutation: Y68F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: psy62 / Gene: CLIBASIA_02120 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 395 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / | ||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.47 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion / pH: 4.6 Details: 0.1M SODIUM ACETATE TRIHYDRATE pH 4.6, 2M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 31, 2015 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→40.8 Å / Num. obs: 45940 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 25.3 Å2 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.84→1.87 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4UDN Resolution: 1.84→40.8 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.515 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 35.228 Å2
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Refinement step | Cycle: 1 / Resolution: 1.84→40.8 Å
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Refine LS restraints |
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