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- PDB-3eka: Crystal structure of the complex of hyaluranidase trimer with asc... -

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Basic information

Entry
Database: PDB / ID: 3eka
TitleCrystal structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sites
ComponentsHyaluronidase, phage associated
KeywordsLYASE / ASCORBIC ACID COMPLEX / HYALURONAN LYASE / PHAGE TAIL FIBRE / TRIPLE-STRANDED
Function / homologyHyaluronidase, bacterial / Hyaluronidase protein (HylP) / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / hyalurononglucosaminidase activity / capsule polysaccharide biosynthetic process / ASCORBIC ACID / Hyaluronidase, phage associated
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMishra, P. / Ethayathulla, A.S. / Prem Kumar, R. / Singh, N. / Sharma, S. / Kaur, P. / Bhakuni, V. / Singh, T.P.
CitationJournal: Febs J. / Year: 2009
Title: Polysaccharide binding sites in hyaluronate lyase--crystal structures of native phage-encoded hyaluronate lyase and its complexes with ascorbic acid and lactose.
Authors: Mishra, P. / Prem Kumar, R. / Ethayathulla, A.S. / Singh, N. / Sharma, S. / Perbandt, M. / Betzel, C. / Kaur, P. / Srinivasan, A. / Bhakuni, V. / Singh, T.P.
History
DepositionSep 19, 2008Deposition site: RCSB / Processing site: PDBJ
SupersessionSep 29, 2009ID: 2PK1
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Hyaluronidase, phage associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3264
Polymers35,7971
Non-polymers5283
Water1,11762
1
A: Hyaluronidase, phage associated
hetero molecules

A: Hyaluronidase, phage associated
hetero molecules

A: Hyaluronidase, phage associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,97712
Polymers107,3923
Non-polymers1,5859
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area60520 Å2
ΔGint-211 kcal/mol
Surface area38850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.502, 58.502, 583.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

21A-386-

HOH

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Components

#1: Protein Hyaluronidase, phage associated /


Mass: 35797.172 Da / Num. of mol.: 1 / Fragment: residues 7-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: hylP1, HYLP2, SPy_0701 / Plasmid: PET 21D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A0M7, hyaluronate lyase
#2: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: TRIS HCL, SODIUM FORMATE, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 203 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2007 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 6874 / Num. obs: 6874 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.11 / Net I/σ(I): 11.7
Reflection shellResolution: 3.1→3.15 Å / Mean I/σ(I) obs: 2.67 / Rsym value: 0.434 / % possible all: 92

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C3F

2c3f


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.878 / SU B: 20.1 / SU ML: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.619 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 516 7.5 %RANDOM
Rwork0.197 ---
all0.212 6874 --
obs0.204 6358 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.59 Å2
Baniso -1Baniso -2Baniso -3
1-4.68 Å22.34 Å20 Å2
2--4.68 Å20 Å2
3----7.02 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 36 62 2613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222585
X-RAY DIFFRACTIONr_angle_refined_deg2.3111.9833487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0955331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.54525.472106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.86915465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7451511
X-RAY DIFFRACTIONr_chiral_restr0.120.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021919
X-RAY DIFFRACTIONr_nbd_refined0.3080.21041
X-RAY DIFFRACTIONr_nbtor_refined0.3320.21761
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.2588
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.294
X-RAY DIFFRACTIONr_mcbond_it1.6721.51684
X-RAY DIFFRACTIONr_mcangle_it2.12522620
X-RAY DIFFRACTIONr_scbond_it3.13731023
X-RAY DIFFRACTIONr_scangle_it4.4894.5867
LS refinement shellResolution: 3.1→3.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 35 -
Rwork0.234 446 -
obs--90.24 %

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