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- PDB-1egu: CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE A... -

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Basic information

Entry
Database: PDB / ID: 1egu
TitleCRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE AT 1.56 A RESOLUTION
ComponentsHYALURONATE LYASE
KeywordsLYASE / (alfa5/alfa5) barrel
Function / homology
Function and homology information


hyaluronate lyase / hyaluronate lyase activity / organic substance catabolic process / hydrolase activity, acting on glycosyl bonds / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
: / Hyaluronate lyase, N-terminal beta-sheet domain / Hyaluronate lyase, beta-sheet domain superfamily / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain ...: / Hyaluronate lyase, N-terminal beta-sheet domain / Hyaluronate lyase, beta-sheet domain superfamily / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitinase Ac; Chain A, domain 3 / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Glycosyltransferase / Alpha/alpha barrel / Galactose-binding-like domain superfamily / Distorted Sandwich / Immunoglobulin E-set / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.56 Å
AuthorsLi, S. / Kelly, S.J. / Lamani, E. / Ferraroni, M. / Jedrzejas, M.J.
CitationJournal: EMBO J. / Year: 2000
Title: Structural basis of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase.
Authors: Li, S. / Kelly, S.J. / Lamani, E. / Ferraroni, M. / Jedrzejas, M.J.
History
DepositionFeb 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYALURONATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7543
Polymers83,5621
Non-polymers1922
Water11,710650
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.041, 104.279, 101.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer in one asymmetry unit.

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Components

#1: Protein HYALURONATE LYASE /


Mass: 83561.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q54873, hyaluronate lyase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 650 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 62% Saturated Ammonium Sulfate, 100 mM Sodium Cacodylate pH6.00, 100 mM Sodium Chloride, 10 mM EDTA, 2% dioxane , VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
pH: 7.4 / Details: Jadrzejas, M.J., (1998) J. Struct. Biol., 121, 73.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.0 mMTris-HCl1drop
22.0 mMEDTA1drop
35 mg/mlenzyme1drop
43.2 Mammonium sulfate1reservoir
5100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9
DetectorType: BRANDEIS - B4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. all: 124955 / Num. obs: 124919 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.1
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.204 / % possible all: 96
Reflection
*PLUS
Num. measured all: 411697
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameVersionClassification
XTALVIEWrefinement
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.56→20 Å / σ(F): 0.001 / σ(I): 0.001 / Stereochemistry target values: Eugh and Huber
Details: X-plor slowcooling with bulksolvant correction at 5000K, slowcooling with torsion angle refinement, baoverall refinement. Three N-terminal residues are present in the working sequence ...Details: X-plor slowcooling with bulksolvant correction at 5000K, slowcooling with torsion angle refinement, baoverall refinement. Three N-terminal residues are present in the working sequence (168Ala, 169Ser, 170Val) but have not been modelled. There were weak electron densities suggesting that GLN892 and HIS893 might be present. This information provides a clue in analyzing which direction the last nine C-terminal residues go.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1232 -random
Rwork0.2 ---
all-124919 --
obs-124919 98.6 %-
Refinement stepCycle: LAST / Resolution: 1.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5794 0 10 650 6454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_d2.38
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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