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- PDB-8hvb: Crystal structure of lacto-N-biosidase StrLNBase from Streptomyce... -

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Basic information

Entry
Database: PDB / ID: 8hvb
TitleCrystal structure of lacto-N-biosidase StrLNBase from Streptomyces sp. strain 142, lacto-N-biose complex
ComponentsLacto-N-biosidase
KeywordsHYDROLASE / Glycoside hydrolase / lacto-N-biosidase / lacto-N-biose complex
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / : / carbohydrate metabolic process
Similarity search - Function
: / Ricin-type beta-trefoil lectin domain-like / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Lectin domain of ricin B chain profile. / Ricin B, lectin domain ...: / Ricin-type beta-trefoil lectin domain-like / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-D-galactopyranose / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Lacto-N-biosidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFushinobu, S. / Yamada, C. / Fujio, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal structure of glycoside hydrolase family 20 lacto-N-biosidase from soil bacterium Streptomyces sp. strain 142
Authors: Fujio, N. / Yamada, C. / Fushinobu, S.
History
DepositionDec 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6363
Polymers66,2351
Non-polymers4012
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint9 kcal/mol
Surface area23280 Å2
Unit cell
Length a, b, c (Å)53.925, 51.344, 86.507
Angle α, β, γ (deg.)90.00, 98.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lacto-N-biosidase


Mass: 66234.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: 142 / Plasmid: pCold-ProS2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Z4I7
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.8 Å3/Da / Density % sol: 31.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.3 M Ammonium fluoride, 10%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.052 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 21, 2022
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.052 Å / Relative weight: 1
ReflectionResolution: 1.6→48.5 Å / Num. obs: 62063 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 12.18 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.057 / Rrim(I) all: 0.153 / Net I/σ(I): 9.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3045 / CC1/2: 0.913 / Rpim(I) all: 0.391 / Rrim(I) all: 1.049 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.621 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18406 3060 4.9 %RANDOM
Rwork0.14918 ---
obs0.1509 58988 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.474 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å20.61 Å2
2--0.69 Å20 Å2
3----0.9 Å2
Refinement stepCycle: 1 / Resolution: 1.6→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4593 0 26 423 5042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124719
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164404
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.6546423
X-RAY DIFFRACTIONr_angle_other_deg0.5421.56810110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8315600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.735542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57910738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021121
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_it1.5041.4822403
X-RAY DIFFRACTIONr_mcbond_other1.5021.4822403
X-RAY DIFFRACTIONr_mcangle_it2.2352.6653002
X-RAY DIFFRACTIONr_mcangle_other2.2362.6663003
X-RAY DIFFRACTIONr_scbond_it2.4581.7532316
X-RAY DIFFRACTIONr_scbond_other2.4581.7532317
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7963.083422
X-RAY DIFFRACTIONr_long_range_B_refined4.62216.795315
X-RAY DIFFRACTIONr_long_range_B_other4.62216.85316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 249 -
Rwork0.182 4319 -
obs--100 %

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