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Open data
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Basic information
Entry | Database: PDB / ID: 1dp0 | ||||||
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Title | E. COLI BETA-GALACTOSIDASE AT 1.7 ANGSTROM | ||||||
![]() | BETA-GALACTOSIDASE | ||||||
![]() | HYDROLASE / TIM BARREL (ALPHA/BETA BARREL) / JELLY-ROLL BARREL / IMMUNOGLOBULIN / BETA SUPERSANDWICH | ||||||
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 | ![]() ![]() | ||||||
![]() | Juers, D.H. / Jacobson, R.H. / Wigley, D. / Zhang, X.J. / Huber, R.E. / Tronrud, D.E. / Matthews, B.W. | ||||||
![]() | ![]() Title: High resolution refinement of beta-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for alpha-complementation. Authors: Juers, D.H. / Jacobson, R.H. / Wigley, D. / Zhang, X.J. / Huber, R.E. / Tronrud, D.E. / Matthews, B.W. #1: ![]() Title: Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between beta-galactosidase and other glycohydrolases Authors: Juers, D.H. / Jacobson, R.H. / Wigley, D. / Zhang, X.J. / Huber, R.E. / Tronrud, D.E. / Matthews, B.W. #2: ![]() Title: Three-dimensional structure of beta-galactosidase from E. coli Authors: Juers, D.H. / Huber, R.E. / Matthews, B.W. #3: ![]() Title: Crystallization of beta-galactosidase from Escherichia coli Authors: Jacobson, R.H. / Zhang, X.J. / DuBose, R.F. / Matthews, B.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 948.2 KB | Display | ![]() |
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PDB format | ![]() | 748.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 534.3 KB | Display | ![]() |
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Full document | ![]() | 668.8 KB | Display | |
Data in XML | ![]() | 193.2 KB | Display | |
Data in CIF | ![]() | 293.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 116506.266 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-DMS / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10 % PEG 8000 100 MM BIS-TRIS 200 MM MGCL(2) 100 MM NACL 10 MM DTT, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 288K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion / Details: used seeding | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 12, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→15 Å / Num. obs: 542319 / % possible obs: 98.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.9 / % possible all: 90.5 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Redundancy: 4.2 % / Num. measured all: 2201152 / Rmerge(I) obs: 0.06 / Biso Wilson estimate: 14.9 Å2 |
Reflection shell | *PLUS % possible obs: 97 % / Mean I/σ(I) obs: 2.9 |
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Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMEN / Resolution: 1.7→15 Å / Isotropic thermal model: NONE USED / Stereochemistry target values: TNT Details: USED CONJUGATE DIRECTION MINIMIZATION OF A LEAST SQUARES RESIDUAL FUNCTION.
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Solvent computation | Solvent model: BABINET'S PRINCIPLE / Bsol: 129 Å2 / ksol: 0.66 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.157 / Rfactor Rwork: 0.157 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |