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- PDB-7eyo: Crystal structure of leech hyaluronidase -

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Basic information

Entry
Database: PDB / ID: 7eyo
TitleCrystal structure of leech hyaluronidase
ComponentsHyaluronoglucuronidase
KeywordsHYDROLASE / Hyaluronidae / GH79
Function / homology
Function and homology information


hyaluronoglucuronidase / hyaluronoglucuronidase activity / hyaluronan catabolic process / extracellular matrix / transferase activity / extracellular space / membrane
Similarity search - Function
Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Hyaluronoglucuronidase
Similarity search - Component
Biological speciesHirudo nipponia (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHuang, H. / Hou, X.D. / Rao, Y.J. / Kang, Z.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000058 China
National Natural Science Foundation of China (NSFC)31970085 China
Other privateBK20200025 China
Other private2018YFA0901400 China
CitationJournal: Carbohydr Polym / Year: 2022
Title: Structure and cleavage pattern of a hyaluronate 3-glycanohydrolase in the glycoside hydrolase 79 family.
Authors: Huang, H. / Hou, X. / Xu, R. / Deng, Z. / Wang, Y. / Du, G. / Rao, Y. / Chen, J. / Kang, Z.
History
DepositionMay 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hyaluronoglucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1555
Polymers56,1221
Non-polymers1,0334
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint14 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.514, 69.474, 86.739
Angle α, β, γ (deg.)90.000, 95.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hyaluronoglucuronidase / LHyal / Hyaluronate 3-glycanohydrolase


Mass: 56122.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo nipponia (invertebrata) / Production host: Komagataella pastoris (fungus) / References: UniProt: X4Y2L4, hyaluronoglucuronidase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: trisodium citrate, ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 43983 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Χ2: 0.912 / Net I/σ(I): 9.2 / Num. measured all: 295605
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.926.30.49641030.9140.210.540.91292.9
1.92-1.996.90.36644310.9580.1490.3950.93499.9
1.99-2.086.80.26143960.9770.1070.2830.95899.9
2.08-2.196.40.19244070.980.0820.209199.8
2.19-2.3370.14444020.9880.0580.1550.99599.9
2.33-2.516.90.11544040.990.0470.1240.95799.8
2.51-2.766.60.09544300.9920.040.1030.9599.9
2.76-3.1670.0844470.9940.0330.0870.90299.9
3.16-3.996.70.06944480.9940.0290.0750.81199.7
3.99-506.50.06345150.9940.0270.0680.70499.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LA4

5la4


Resolution: 1.85→43.32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.049 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 2024 4.7 %RANDOM
Rwork0.1775 ---
obs0.1791 40596 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.03 Å2 / Biso mean: 23.858 Å2 / Biso min: 6.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.07 Å2
2---0.03 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.85→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 68 397 4319
Biso mean--32.48 32.81 -
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134013
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173638
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.6625443
X-RAY DIFFRACTIONr_angle_other_deg1.4231.6038478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1475485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92424.202188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84615677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0541510
X-RAY DIFFRACTIONr_chiral_restr0.080.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024430
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02832
LS refinement shellResolution: 1.85→1.896 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.329 103 -
Rwork0.241 2218 -
obs--70.94 %

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