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

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Basic information

Entry
Database: PDB / ID: 8hvd
TitleCrystal structure of lacto-N-biosidase StrLNBase from Streptomyces sp. strain 142, galacto-N-biose complex 2
ComponentsLacto-N-biosidase
KeywordsHYDROLASE / Glycoside hydrolase / lacto-N-biosidase / galacto-N-biose complex 2
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
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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

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Assembly

Deposited unit
A: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6182
Polymers66,2351
Non-polymers3831
Water13,421745
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint11 kcal/mol
Surface area23440 Å2
Unit cell
Length a, b, c (Å)52.779, 60.825, 88.232
Angle α, β, γ (deg.)90.00, 98.19, 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: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.25 M Ammonium fluoride, 12.5%(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: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 28, 2022
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid, nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→47.99 Å / Num. obs: 107633 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 10.69 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.033 / Rrim(I) all: 0.061 / Net I/σ(I): 12.4
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 16650 / CC1/2: 0.784 / Rpim(I) all: 0.324 / Rrim(I) all: 0.583 / % 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: 1.41→47.94 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.22 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19273 5355 5 %RANDOM
Rwork0.16455 ---
obs0.16594 102255 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0 Å20.06 Å2
2--1.3 Å20 Å2
3----0.78 Å2
Refinement stepCycle: 1 / Resolution: 1.41→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4598 0 26 745 5369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0124736
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164422
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.6546449
X-RAY DIFFRACTIONr_angle_other_deg0.5721.56810154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2455603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.951542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13510742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021123
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_it1.5721.5272412
X-RAY DIFFRACTIONr_mcbond_other1.5651.5272412
X-RAY DIFFRACTIONr_mcangle_it2.2492.7453015
X-RAY DIFFRACTIONr_mcangle_other2.2482.7473016
X-RAY DIFFRACTIONr_scbond_it2.2321.6512324
X-RAY DIFFRACTIONr_scbond_other2.2311.6512325
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3372.9413435
X-RAY DIFFRACTIONr_long_range_B_refined4.68317.365657
X-RAY DIFFRACTIONr_long_range_B_other4.68317.365658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.41→1.441 Å
RfactorNum. reflection% reflection
Rfree0.285 403 -
Rwork0.258 7522 -
obs--99.95 %

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