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- PDB-1rwf: Crystal structure of Arthrobacter aurescens chondroitin AC lyase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rwf | |||||||||
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Title | Crystal structure of Arthrobacter aurescens chondroitin AC lyase in complex with chondroitin tetrasaccharide | |||||||||
![]() | chondroitin AC lyase | |||||||||
![]() | LYASE / chondroitinase / chondroitin / chondroitin lyase | |||||||||
Function / homology | ![]() carbohydrate binding / carbohydrate metabolic process / lyase activity / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lunin, V.V. / Li, Y. / Miyazono, H. / Kyogashima, M. / Bell, A.W. / Cygler, M. | |||||||||
![]() | ![]() Title: High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism Authors: Lunin, V.V. / Li, Y. / Linhardt, R.J. / Miyazono, H. / Kyogashima, M. / Kaneko, T. / Bell, A.W. / Cygler, M. | |||||||||
History |
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Remark 600 | HETEROGEN SUGAR CHAIN D (GAD 809)-(NGL 810)-(GCT 811)-(NGL 812) IS CHONDROITIN SULFATE TETRASACCHARIDE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 335.4 KB | Display | ![]() |
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PDB format | ![]() | 269.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 834.1 KB | Display | ![]() |
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Full document | ![]() | 842 KB | Display | |
Data in XML | ![]() | 38.3 KB | Display | |
Data in CIF | ![]() | 61.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rw9SC ![]() 1rwaC ![]() 1rwcC ![]() 1rwgC ![]() 1rwhC 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
#1: Protein | Mass: 79863.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Polysaccharide | 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D- ...2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-2,6-anhydro-3-deoxy-L-xylo-hexonic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 8000, ammonium acetate, glycerol, phosphate buffer, 30 seconds soaking time, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→50 Å / Num. obs: 146507 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rsym value: 0.081 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.41→1.46 Å / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RW9 Resolution: 1.45→27.12 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.942 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→27.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20 /
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