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- PDB-4d0q: Hyaluronan Binding Module of the Streptococcal Pneumoniae Hyaluro... -

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Basic information

Entry
Database: PDB / ID: 4d0q
TitleHyaluronan Binding Module of the Streptococcal Pneumoniae Hyaluronate Lyase
ComponentsHYALURONATE LYASE
KeywordsLYASE / HYALURONAN BINDING CARBOHYDRATE BINDING MODULE / CBM / PL FAMILY 8 / PL8 / HYL
Function / homology
Function and homology information


hyaluronate lyase / hyaluronate lyase activity / : / 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 / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSTREPTOCOCCUS PNEUMONIAE TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsSuits, M.D.L. / Pluvinage, B. / Law, A. / Liu, Y. / Palma, A.S. / Chai, W. / Feizi, T. / Boraston, A.B.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Conformational Analysis of the Streptococcus Pneumoniae Hyaluronate Lyase and Characterization of its Hyaluronan-Specific Carbohydrate-Binding Module.
Authors: Suits, M.D.L. / Pluvinage, B. / Law, A. / Liu, Y. / Palma, A.S. / Chai, W. / Feizi, T. / Boraston, A.B.
History
DepositionApr 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: HYALURONATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,60710
Polymers19,0481
Non-polymers5599
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.440, 60.800, 35.470
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HYALURONATE LYASE / HYALURONIDASE / HYASE


Mass: 19048.338 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 54-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE TIGR4 (bacteria)
Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q54873, hyaluronate lyase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1,2-ETHANEDIOL (EDO): WAS ADDED AS THE CRYOPROTECTANT.

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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: 2.06 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: BY THE SITTING DROP VAPOUR DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF THE PROTEIN SOLUTION WITH A MOTHER LIQUOR CONSISTING OF 18% (W/V) POLYETHYLENE GLYCOL 3,350 AND 0.1 M SODIUM ACETATE (PH 5.5) AT 292 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.95371
DetectorType: MARRESEARCH MX300HE / Detector: CCD / Date: Feb 22, 2012 / Details: MIRRORS
RadiationMonochromator: KOHZU DOUBLE CRYSTAL MONOCHROMATOR (DCM), FEATURING INDIRECTLY WATER- COOLED FIRST CRYSTAL AND FLAT, LONG SECOND CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 1.2→35.3 Å / Num. obs: 45456 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.7
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.5 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.2→35.31 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.452 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. TRP 82, A KEY RESIDUE IN THE CARBOHYDRATE RECOGNITION SITE IS SHOWN IN TWO CONFORMATIONS THAT BOTH CORRESPOND TO LOW OCCUPANCIES.
RfactorNum. reflection% reflectionSelection details
Rfree0.15939 2281 5 %RANDOM
Rwork0.12715 ---
obs0.12878 42890 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.854 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20.8 Å2
2---0.08 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 36 216 1516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021389
X-RAY DIFFRACTIONr_bond_other_d0.0010.021395
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9521871
X-RAY DIFFRACTIONr_angle_other_deg2.98333182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021542
X-RAY DIFFRACTIONr_gen_planes_other0.010.02302
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7720.727663
X-RAY DIFFRACTIONr_mcbond_other1.4680.719662
X-RAY DIFFRACTIONr_mcangle_it2.1861.096832
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3461.202726
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.62932784
X-RAY DIFFRACTIONr_sphericity_free46.307560
X-RAY DIFFRACTIONr_sphericity_bonded16.63652914
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 162 -
Rwork0.201 2945 -
obs--92.64 %
Refinement TLS params.Method: refined / Origin x: 7.546 Å / Origin y: -9.087 Å / Origin z: 6.737 Å
111213212223313233
T0.0613 Å20 Å2-0.0061 Å2-0.0578 Å20.0005 Å2--0.0018 Å2
L0.1508 °2-0.0085 °20.0053 °2-0.0962 °20.021 °2--0.0175 °2
S0 Å °0.0006 Å °0.0059 Å °0.0011 Å °0.002 Å °0.0037 Å °-0.0016 Å °0.001 Å °-0.002 Å °

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