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- PDB-4dxb: 2.29A structure of the engineered MBP TEM-1 fusion protein RG13 i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dxb | ||||||
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Title | 2.29A structure of the engineered MBP TEM-1 fusion protein RG13 in complex with zinc, P1 space group | ||||||
![]() | Maltose-binding periplasmic protein, Beta-lactamase TEM chimera | ||||||
![]() | SUGAR BINDING PROTEIN / HYDROLASE / TEM / beta-lactamase / MBP / allosteric regulation / zinc binding / maltose binding | ||||||
Function / homology | ![]() detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / beta-lactam antibiotic catabolic process / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / beta-lactam antibiotic catabolic process / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / periplasmic space / response to antibiotic / DNA damage response / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van den Akker, F. / Ke, W. | ||||||
![]() | ![]() Title: Structure of an Engineered beta-Lactamase Maltose Binding Protein Fusion Protein: Insights into Heterotropic Allosteric Regulation. Authors: Ke, W. / Laurent, A.H. / Armstrong, M.D. / Chen, Y. / Smith, W.E. / Liang, J. / Wright, C.M. / Ostermeier, M. / van den Akker, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 261.2 KB | Display | ![]() |
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PDB format | ![]() | 209 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.8 KB | Display | ![]() |
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Full document | ![]() | 445.6 KB | Display | |
Data in XML | ![]() | 48.3 KB | Display | |
Data in CIF | ![]() | 68.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dxcC ![]() 1ompS ![]() 1zg4S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 69937.273 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0AEX9, UniProt: P62593, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Sequence details | RG13 IS A CHIMERA COMPRISING THE N-TERMINAL DOMAIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN (UNP ...RG13 IS A CHIMERA COMPRISING | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: A 1.0 uL drop was prepared using 0.5 uL protein mixture (13.8 mg/mL RG13, 2.5 mM zinc chloride) and 0.5 uL reservoir solution (0.2 M ammonium acetate, 0.1 M Tris, pH 8.5-9.5, 15-30% PEG3350) ...Details: A 1.0 uL drop was prepared using 0.5 uL protein mixture (13.8 mg/mL RG13, 2.5 mM zinc chloride) and 0.5 uL reservoir solution (0.2 M ammonium acetate, 0.1 M Tris, pH 8.5-9.5, 15-30% PEG3350) and equilibrated over a 1 ml reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2007 / Details: mirrors | |||||||||
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.29→31.45 Å / Num. all: 62117 / Num. obs: 59138 / % possible obs: 56.8 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.054 | |||||||||
Reflection shell | Resolution: 2.29→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5876 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1ZG4 AND 1OMP Resolution: 2.29→31.45 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.874 / SU B: 8.733 / SU ML: 0.22 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.461 / ESU R Free: 0.297 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.401 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→31.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.354 Å / Total num. of bins used: 20
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