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Open data
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Basic information
Entry | Database: PDB / ID: 3iap | ||||||
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Title | E. coli (lacZ) beta-galactosidase (E416Q) | ||||||
![]() | Beta-galactosidase | ||||||
![]() | HYDROLASE / Glu-416-Gln BETA-GALACTOSIDASE HYDROLASE 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 | ![]() ![]() ![]() | ||||||
![]() | Lo, S. / Dugdale, M.L. / Jeerh, N. / Ku, T. / Roth, N.J. / Huber, R.E. | ||||||
![]() | ![]() Title: Studies of Glu-416 variants of beta-galactosidase (E. coli) show that the active site Mg(2+) is not important for structure and indicate that the main role of Mg (2+) is to mediate ...Title: Studies of Glu-416 variants of beta-galactosidase (E. coli) show that the active site Mg(2+) is not important for structure and indicate that the main role of Mg (2+) is to mediate optimization of active site chemistry Authors: Lo, S. / Dugdale, M.L. / Jeerh, N. / Ku, T. / Roth, N.J. / Huber, R.E. #1: ![]() Title: Crystallography & NMR System | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 921.2 KB | Display | ![]() |
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PDB format | ![]() | 742.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 532.2 KB | Display | ![]() |
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Full document | ![]() | 569.8 KB | Display | |
Data in XML | ![]() | 172.6 KB | Display | |
Data in CIF | ![]() | 262 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3iaqC ![]() 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 , 1 types, 4 molecules ABCD
#1: Protein | Mass: 116505.281 Da / Num. of mol.: 4 / Fragment: BETA-GALACTOSIDASE / Mutation: E416Q Source method: isolated from a genetically manipulated source Details: N-terminal His tag / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B8LFD6, UniProt: P00722*PLUS, beta-galactosidase |
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-Non-polymers , 5 types, 3985 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-BTB / #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: 2.66 Å3/Da / Density % sol: 53.78 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, NaCl, MgCl2, DTT, Bis-Tris, pH6.5, HANGING DROP AT 288K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 17, 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: 1.11589 Å / Relative weight: 1 |
Reflection | Resolution: 2→58.42 Å / Num. all: 395192 / Num. obs: 120198 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.29 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.198 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.5 / Num. unique all: 58195 / Rsym value: 0.539 / % possible all: 90.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1DP0 Resolution: 2→53.38 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.695 / SU ML: 0.104 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.187 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 24.347 Å2
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Refinement step | Cycle: LAST / Resolution: 2→53.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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