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- PDB-1ofz: Crystal structure of fungal lectin : six-bladed beta-propeller fo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ofz | ||||||
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Title | Crystal structure of fungal lectin : six-bladed beta-propeller fold and novel fucose recognition mode for aleuria aurantia lectin | ||||||
![]() | FUCOSE-SPECIFIC LECTIN | ||||||
![]() | SUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / LECTIN / AAL / FUCOSE / ALEURIA AURANTIA LECTIN | ||||||
Function / homology | ![]() reproductive fruiting body development / fucose binding / defense response to fungus / carbohydrate binding / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wimmerova, M. / Mitchell, E. / Sanchez, J.F. / Gautier, C. / Imberty, A. | ||||||
![]() | ![]() Title: Crystal Structure of Fungal Lectin: Six-Bladed {Beta}-Propeller Fold and Novel Fucose Recognition Mode for Aleuria Aurantia Lectin Authors: Wimmerova, M. / Mitchell, E. / Sanchez, J.F. / Gautier, C. / Imberty, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.1 KB | Display | ![]() |
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PDB format | ![]() | 127.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.3 KB | Display | ![]() |
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Full document | ![]() | 478.7 KB | Display | |
Data in XML | ![]() | 37.1 KB | Display | |
Data in CIF | ![]() | 59.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.6857, 0.6241, 0.3745), Vector: |
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Components
#1: Protein | Mass: 33454.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Sugar | ChemComp-FUL / #3: Sugar | ChemComp-FUC / #4: Water | ChemComp-HOH / | Sequence details | P18891 HAS RESIDUE 139 AS GLY AND 163 AS VAL. ELECTRON DENSITY OF MOLECULE CRYSTALLISED INDICATES ...P18891 HAS RESIDUE 139 AS GLY AND 163 AS VAL. ELECTRON DENSITY OF MOLECULE CRYSTALLIS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 32.8 % Description: DATA WERE COLLECTED AT ENERGY REMOTE FROM THE MERCURY ANOMALOUS EDGE | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 2UL BUFFER (0.1 M SODIUM CACODYLATE PH 6.5, 0.2M MAGNESIUM ACETATE TETRAHYDRATE, 20% PEG 8000) PLUS 2UL OF LECTIN PROTEIN AT 10 MG/ML AND L-FUCOSE AT 137 UG/ML | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density Matthews: 2.2 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: ADSC CCD / Detector: CCD / Date: Jan 15, 2003 / Details: MULTILAYER |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.96 Å / Num. obs: 534572 / % possible obs: 96.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 18.4 / % possible all: 96.8 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. obs: 94102 / Redundancy: 3.6 % / Num. measured all: 534572 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / % possible obs: 96.8 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 1.9 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.5→19.96 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.417 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY WITH OCCUPANCY SET TO ZERO.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.96 Å
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