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- PDB-3e1f: E.Coli (lacZ) beta-galactosidase (H418E) in complex with galactose -
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Open data
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Basic information
Entry | Database: PDB / ID: 3e1f | ||||||
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Title | E.Coli (lacZ) beta-galactosidase (H418E) in complex with galactose | ||||||
![]() | Beta-galactosidase | ||||||
![]() | HYDROLASE / His-418-Glu BETA-GALACTOSIDASE HYDROLASE TIM BARREL (ALPHA/BETA BARREL) JELLY-ROLL BARREL IMMUNOGLOBULIN BETA SUPERSANDWICH / Glycosidase | ||||||
Function / homology | ![]() alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huber, R.E. / Dugdale, M.L. | ||||||
![]() | ![]() Title: Direct and indirect roles of His-418 in metal binding and in the activity of beta-galactosidase (E. coli). Authors: Juers, D.H. / Rob, B. / Dugdale, M.L. / Rahimzadeh, N. / Giang, C. / Lee, M. / Matthews, B.W. / Huber, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 811.6 KB | Display | ![]() |
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PDB format | ![]() | 661.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 531.5 KB | Display | ![]() |
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Full document | ![]() | 604.5 KB | Display | |
Data in XML | ![]() | 145.5 KB | Display | |
Data in CIF | ![]() | 197 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dymC ![]() 3dyoC ![]() 3dypC ![]() 1jyxS C: citing same article ( 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 12 molecules 1234![](data/chem/img/GAL.gif)
![](data/chem/img/GAL.gif)
#1: Protein | Mass: 116497.234 Da / Num. of mol.: 4 / Fragment: BETA-GALACTOSIDASE / Mutation: H418E Source method: isolated from a genetically manipulated source Details: N-terminal His tag / Source: (gene. exp.) ![]() ![]() ![]() ![]() #5: Sugar | ChemComp-GAL / |
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-Non-polymers , 4 types, 424 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-DMS / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.68 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2007 / Details: KOHZU: Double Crystal Si (111) |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11588 Å / Relative weight: 1 |
Reflection | Resolution: 3→98.54 Å / Num. all: 90713 / Num. obs: 90713 / Observed criterion σ(F): 0 / Limit h max: 41 / Limit h min: -42 / Limit k max: 50 / Limit k min: -42 / Limit l max: 44 / Limit l min: 0 / Observed criterion F max: 2426618.92 / Observed criterion F min: 43.396 |
Reflection shell | Highest resolution: 3 Å / Num. unique all: 90713 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1JYX Resolution: 3→98.54 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 32496 Nonpolymer 411 Solvent 324 CNS ...Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 32496 Nonpolymer 411 Solvent 324 CNS Parameter files: CNS_TOPPAR/protein_rep.param CNS_TOPPAR/water.param CNS_TOPPAR/ion.param ../cns_1/dms_xplor_par.txt ../cns_1/gal_xplor_par.txt CNS Topology files: CNS_TOPPAR/protein.top CNS_TOPPAR/water.top CNS_TOPPAR/ion.top ../cns_1/dms_xplor_par.txt ../cns_1/gal_xplor_top.txt
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 25.6967 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.93 Å2 / Biso mean: 43.38 Å2 / Biso min: 1.31 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→98.54 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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