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- PDB-1j1n: Structure Analysis of AlgQ2, A Macromolecule(Alginate)-Binding Pe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j1n | |||||||||
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Title | Structure Analysis of AlgQ2, A Macromolecule(Alginate)-Binding Periplasmic Protein Of Sphingomonas Sp. A1., Complexed with an Alginate Tetrasaccharide | |||||||||
![]() | AlgQ2 | |||||||||
![]() | SUGAR BINDING PROTEIN / ALGINATE | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Momma, K. / Mikami, B. / Mishima, Y. / Hashimoto, W. / Murata, K. | |||||||||
![]() | ![]() Title: Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1, complexed with an alginate tetrasaccharide at 1.6-A resolution Authors: Mishima, Y. / Momma, K. / Hashimoto, W. / Mikami, B. / Murata, K. #1: ![]() Title: Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1 at 2.0A resolution Authors: Momma, K. / Mikami, B. / Mishima, Y. / Hashimoto, W. / Murata, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230.3 KB | Display | ![]() |
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PDB format | ![]() | 181.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 500.8 KB | Display | ![]() |
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Full document | ![]() | 512.1 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kwhS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 57251.715 Da / Num. of mol.: 2 / Fragment: residues 1-492 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, ammmonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal grow | *PLUS Details: Momma, K., (2002) J. Mol. Biol., 316, 1061. |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: OXFORD / Detector: CCD / Date: Mar 29, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→61.57 Å / Num. all: 512032 / Num. obs: 159065 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.7 Å2 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 98.7 |
Reflection | *PLUS Lowest resolution: 61.6 Å / Num. obs: 175841 / % possible obs: 98.3 % / Redundancy: 7.4 % / Num. measured all: 559708 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 94.6 % / Num. unique obs: 16776 / Num. measured obs: 47676 / Rmerge(I) obs: 0.242 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: apo AlgQ2 (1KWH) Resolution: 1.6→28.73 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1784538.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.5841 Å2 / ksol: 0.377847 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→28.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 61.6 Å / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.65 Å / Rfactor Rwork: 0.22 / Num. reflection Rwork: 12879 |