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Open data
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Basic information
Entry | Database: PDB / ID: 3i3d | ||||||
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Title | E. COLI (lacZ) BETA-GALACTOSIDASE (M542A) IN COMPLEX WITH IPTG | ||||||
![]() | Beta-galactosidase | ||||||
![]() | HYDROLASE / BETA-GALACTOSIDASE / TIM BARREL (ALPHA/BETA BARREL) / JELLY-ROLL BARREL / IMMUNOGLOBULIN BETA SUPERSANDWHICH / 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 | ![]() ![]() ![]() | ||||||
![]() | Dugdale, M.L. / Dymianiw, D. / Minhas, B. / Huber, R.E. | ||||||
![]() | ![]() Title: Role of Met-542 as a guide for the conformational changes of Phe-601 that occur during the reaction of β-galactosidase (Escherichia coli). Authors: Dugdale, M.L. / Dymianiw, D.L. / Minhas, B.K. / D'Angelo, I. / 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 | ![]() | 908.5 KB | Display | ![]() |
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PDB format | ![]() | 735 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3i3bC ![]() 3i3eC ![]() 1dp0S 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 10 molecules ABCD![](data/chem/img/IPT.gif)
![](data/chem/img/IPT.gif)
#1: Protein | Mass: 116446.156 Da / Num. of mol.: 4 / Fragment: Residues 10-1024 / Mutation: M543A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B8LFD6, UniProt: P00722*PLUS, beta-galactosidase #2: Sugar | ChemComp-IPT / |
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-Non-polymers , 4 types, 3712 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)
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: 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: 2.69 Å3/Da / Density % sol: 54.29 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, NaCl, MgCl2, DTT, Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 8, 2008 / 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: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→61.97 Å / Num. all: 253403 / Num. obs: 253403 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.82 % / Biso Wilson estimate: 14.1 Å2 / Limit h max: 68 / Limit h min: 0 / Limit k max: 73 / Limit k min: 0 / Limit l max: 92 / Limit l min: 0 / Observed criterion F max: 5745979.82 / Observed criterion F min: 25.836 / Rmerge(I) obs: 0.152 / Rsym value: 0.18 / Net I/σ(I): 9.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1DP0 Resolution: 2.2→61.97 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.88 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 59.9845 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.24 Å2 / Biso mean: 20.88 Å2 / Biso min: 1.44 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→61.97 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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