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Open data
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Basic information
Entry | Database: PDB / ID: 1nxd | ||||||
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Title | Crystal structure of MnMn Concanavalin A | ||||||
![]() | concanavalin A | ||||||
![]() | METAL BINDING PROTEIN / Lectin | ||||||
Function / homology | ![]() regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lopez-Jaramillo, F.J. / Gonzalez-Ramirez, L.A. / Albert, A. / Santoyo-Gonzalez, F. / Vargas-Berenguel, A. / Otalora, F. | ||||||
![]() | ![]() Title: Structure of concanavalin A at pH 8: bound solvent and crystal contacts. Authors: Lopez-Jaramillo, F.J. / Gonzalez-Ramirez, L.A. / Albert, A. / Santoyo-Gonzalez, F. / Vargas-Berenguel, A. / Otalora, F. #1: ![]() Title: Crystallization and cryocrystallography inside X-ray capillaries Authors: Lopez-Jaramillo, F.J. / Garcia-Ruiz, J.M. / Gavira, J.A. / Otalora, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.2 KB | Display | ![]() |
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PDB format | ![]() | 173 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1nlsS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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7 | ![]()
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8 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules 1234
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 817 molecules ![](data/chem/img/AZI.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-AZI / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 61.78 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: gel acupuncture method (game) / pH: 8 Details: PEG 6000, Sodium Chloride, Calcium Chloride, Manganese Chloride, Sodium Azide, Tris-HCl , pH 8, Gel Acupuncture Method (GAME), temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→19.61 Å / Num. all: 120751 / Num. obs: 120751 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Redundancy: 2.88 % / Biso Wilson estimate: 21.67 Å2 / Limit h max: 54 / Limit h min: 0 / Limit k max: 63 / Limit k min: 0 / Limit l max: 134 / Limit l min: 0 / Observed criterion F max: 7393670.09 / Observed criterion F min: 64.53 / Rsym value: 0.021 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 1.8→2 Å / Redundancy: 2.57 % / Mean I/σ(I) obs: 16.71 / Num. unique all: 24782 / Rsym value: 0.052 / % possible all: 66.8 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 19 Å / Num. obs: 111379 / % possible obs: 94.9 % / Num. measured all: 324343 / Rmerge(I) obs: 0.02 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 93 % / Num. unique obs: 15414 / Num. measured obs: 40384 / Rmerge(I) obs: 0.048 / Mean I/σ(I) obs: 18.15 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1NLS Resolution: 1.9→19 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 50.299 Å2 / ksol: 0.398921 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.09 Å2 / Biso mean: 18.96 Å2 / Biso min: 5.56 Å2
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Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.006
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 19 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.19 / Rfactor Rwork: 0.19 |