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- PDB-1hm3: ACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE ... -

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Basic information

Entry
Database: PDB / ID: 1hm3
TitleACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE OF ENZYME-OLIGOSACCHARIDE COMPLEXES AND MUTAGENESIS
ComponentsCHONDROITINASE AC
KeywordsLYASE / protein-oligosaccharide complex / active site / catalysis
Function / homologyGalactose mutarotase-like domain superfamily / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase 8 / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, C-terminal / Chondroitin AC/alginate lyase / Glycoside hydrolase-type carbohydrate-binding ...Galactose mutarotase-like domain superfamily / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase 8 / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, C-terminal / Chondroitin AC/alginate lyase / Glycoside hydrolase-type carbohydrate-binding / Polysaccharide lyase family 8-like, C-terminal / chondroitin AC lyase / chondroitin AC lyase activity / carbohydrate binding / carbohydrate metabolic process / extracellular region / metal ion binding / Chondroitinase-AC
Function and homology information
Specimen sourcePedobacter heparinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / 2.1 Å resolution
AuthorsHuang, W. / Boju, L. / Tkalec, L. / Su, H. / Yang, H.O. / Gunay, N.S. / Linhardt, R.J. / Kim, Y.S. / Matte, A. / Cygler, M.
CitationJournal: Biochemistry / Year: 2001
Title: Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis.
Authors: Huang, W. / Boju, L. / Tkalec, L. / Su, H. / Yang, H.O. / Gunay, N.S. / Linhardt, R.J. / Kim, Y.S. / Matte, A. / Cygler, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 4, 2000 / Release: May 2, 2001
RevisionDateData content typeGroupProviderType
1.0May 2, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHONDROITINASE AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,65812
Polyers79,7981
Non-polymers1,86111
Water5,873326
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)86.900, 86.900, 192.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP 43 21 2

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide CHONDROITINASE AC


Mass: 79797.703 Da / Num. of mol.: 1 / Source: (gene. exp.) Pedobacter heparinus (bacteria) / Genus: Pedobacter / Genus (production host): Pedobacter / Production host: Pedobacter heparinus (bacteria) / References: UniProt: Q59288, chondroitin AC lyase

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Non-polymers , 9 types, 337 molecules

#2: Chemical ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 2 / Formula: C6H12O6
#3: Chemical ChemComp-RAM / ALPHA-L-RHAMNOSE


Mass: 164.156 Da / Num. of mol.: 2 / Formula: C6H12O5 / Rhamnose
#4: Chemical ChemComp-GCU / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 2 / Formula: C6H10O7 / Glucuronic acid
#5: Chemical ChemComp-XYP / BETA-D-XYLOPYRANOSE


Mass: 150.130 Da / Num. of mol.: 1 / Formula: C5H10O5
#6: Chemical ChemComp-MXY / 2-O-METHYL FUCOSE


Mass: 178.183 Da / Num. of mol.: 1 / Formula: C7H14O5
#7: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6 / N-Acetylglucosamine
#8: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 1 / Formula: C6H10O7 / Glucuronic acid
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca / Calcium
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 / Density percent sol: 45.91 %
Crystal growTemp: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, sodium acetate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
115 %(w/v)PEG33501reservoir
2400 mMsodium acetate1reservoir
3100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: NSLS BEAMLINE X8C / Synchrotron site: NSLS / Beamline: X8C / Wavelength: 1.007
DetectorType: ADSC QUANTUM 4 / Details: mirrors / Detector: CCD / Collection date: Feb 2, 1999
RadiationMonochromator: Graphite / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionD resolution high: 2.1 Å / D resolution low: 20 Å / Number obs: 43620 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.0082 / NetI over sigmaI: 14 / Percent possible obs: 99.3
Reflection shellRmerge I obs: 0.269 / Highest resolution: 2.1 Å / Percent possible all: 98
Reflection
*PLUS
Number measured all: 265815
Reflection shell
*PLUS
Percent possible obs: 98

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefineMethod to determine structure: FOURIER SYNTHESIS / R Free selection details: random / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.254 / R factor R work: 0.226 / Highest resolution: 2.1 Å / Lowest resolution: 2 Å / Number reflection R free: 1280 / Number reflection obs: 45189
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 5382 / Nucleic acid: 0 / Ligand: 114 / Solvent: 326 / Total: 5822

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