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- PDB-1f1s: CRYSTAL STRUCTURE OF STREPTOCOCCUS AGALACTIAE HYALURONATE LYASE A... -

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Basic information

Entry
Database: PDB / ID: 1f1s
TitleCRYSTAL STRUCTURE OF STREPTOCOCCUS AGALACTIAE HYALURONATE LYASE AT 2.1 ANGSTROM RESOLUTION.
ComponentsHYALURONATE LYASE
KeywordsLYASE / The structure consists of three distinct structural domains: two beta domains at two terminals and one alpha domain in the middle of the sequence.
Function / homology
Function and homology information


hyaluronate lyase / hyaluronate lyase activity / : / 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 / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / 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 agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsLi, S. / Jedrzejas, M.J.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Hyaluronan binding and degradation by Streptococcus agalactiae hyaluronate lyase.
Authors: Li, S. / Jedrzejas, M.J.
History
DepositionMay 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYALURONATE LYASE


Theoretical massNumber of molelcules
Total (without water)92,5101
Polymers92,5101
Non-polymers00
Water9,692538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.265, 156.765, 237.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1367-

HOH

DetailsThe biological assembly is one monomer in one asymmetric unit.

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Components

#1: Protein HYALURONATE LYASE /


Mass: 92510.344 Da / Num. of mol.: 1 / Fragment: SEQUENCE FROM 171 TO 984
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q53591, hyaluronate lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 5500 MME, KSCN, Cacodylate., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 8
Details: Jedrzejas, M.J., (2000) Acta Crystallogr., Sect.D, 56, 460.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMcacodylate1reservoirpH6.0
230 mMKSCN1reservoir
319 %PEG5000 MME1reservoir
410 mg/mlprotein1drop
510 mMHEPES1drop
62 mMEDTA1droppH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: BRANDEIS / Detector: CCD / Date: Oct 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 56571 / Num. obs: 54880 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.59 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 1.94 % / Rmerge(I) obs: 0.177 / Num. unique all: 1959 / % possible all: 69.3
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 484052 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 77.2 % / Rmerge(I) obs: 0.172

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→20 Å / σ(F): 0.001 / σ(I): 0.001 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1015 -random
Rwork0.1908 ---
obs-54027 94.1 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6513 0 0 538 7051
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.145
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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