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- PDB-1n7n: Streptococcus pneumoniae Hyaluronate Lyase W292A Mutant -

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Basic information

Entry
Database: PDB / ID: 1n7n
TitleStreptococcus pneumoniae Hyaluronate Lyase W292A Mutant
ComponentsHYALURONIDASE
KeywordsLYASE / protein mutant
Function / homology
Function and homology information


hyaluronate lyase / hyaluronate lyase activity / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Hyaluronate lyase, beta-sheet domain superfamily / : / Hyaluronate lyase, N-terminal beta-sheet domain / : / BppA domain 1 / 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 ...Hyaluronate lyase, beta-sheet domain superfamily / : / Hyaluronate lyase, N-terminal beta-sheet domain / : / BppA domain 1 / 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 / Chondroitinase Ac; Chain A, domain 3 / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / 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 / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNukui, M. / Taylor, K.B. / McPherson, D.T. / Shigenaga, M. / Jedrzejas, M.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The function of hydrophobic residues in the catalytic cleft of Streptococcus pneumoniae hyaluronate lyase. Kinetic characterization of mutant enzyme forms
Authors: Nukui, M. / Taylor, K.B. / McPherson, D.T. / Shigenaga, M. / Jedrzejas, M.J.
History
DepositionNov 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYALURONIDASE


Theoretical massNumber of molelcules
Total (without water)82,2031
Polymers82,2031
Non-polymers00
Water13,187732
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.069, 103.584, 101.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HYALURONIDASE / HYALURONATE LYASE


Mass: 82202.508 Da / Num. of mol.: 1 / Mutation: W292A mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q54873, hyaluronate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15.10 mg/mlprotein1drop
260-65 %satammonium sulfate1reservoir
30.2 M1reservoirNaCl
42 %dioxane1reservoir
550 mMsodium citrate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 10, 2002
RadiationMonochromator: SI crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 125637 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.807 / % possible all: 87.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 125839 / Num. measured all: 636169
Reflection shell
*PLUS
% possible obs: 87.5 %

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Processing

Software
NameClassification
MADNESSdata collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
MADNESSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LOH

1loh


Resolution: 1.55→20 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.209 1237 1 %
Rwork0.18 --
obs0.18 125637 -
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5775 0 0 732 6507
LS refinement shellResolution: 1.55→1.61 Å
RfactorNum. reflection% reflection
Rfree0.295 28 -
obs--87.5 %
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 1 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.015
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.35
LS refinement shell
*PLUS
Rfactor Rwork: 0.28

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