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Yorodumi- PDB-1rwh: Crystal structure of Arthrobacter aurescens chondroitin AC lyase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rwh | |||||||||
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Title | Crystal structure of Arthrobacter aurescens chondroitin AC lyase in complex with chondroitin tetrasaccharide | |||||||||
Components | chondroitin AC lyase | |||||||||
Keywords | LYASE / chondroitinase / chondroitin / chondroitin lyase | |||||||||
Function / homology | Function and homology information carbohydrate binding / lyase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Arthrobacter aurescens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||
Authors | Lunin, V.V. / Li, Y. / Miyazono, H. / Kyogashima, M. / Bell, A.W. / Cygler, M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rwh.cif.gz | 341.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rwh.ent.gz | 274.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/1rwh ftp://data.pdbj.org/pub/pdb/validation_reports/rw/1rwh | HTTPS FTP |
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-Related structure data
Related structure data | 1rw9SC 1rwaC 1rwcC 1rwfC 1rwgC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 79863.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arthrobacter aurescens (bacteria) / References: UniProt: P84141, chondroitin AC lyase |
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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 |
-Non-polymers , 4 types, 1112 molecules
#3: Chemical | ChemComp-NA / | ||
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#4: Chemical | ChemComp-PO4 / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.68 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 8000, ammonium acetate, glycerol, phosphate buffer, 10 hours 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: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9787 Å |
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: 1.25→50 Å / Num. obs: 188554 / % possible obs: 90.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rsym value: 0.058 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.25→1.29 Å / % possible all: 56.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RW9 Resolution: 1.25→25.24 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.477 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.034 / 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: 13.093 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→25.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20 /
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