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- PDB-7v6m: Crystal structure of lacto-N-biosidase TnX from Tynzenella nexili... -

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Basic information

Entry
Database: PDB / ID: 7v6m
TitleCrystal structure of lacto-N-biosidase TnX from Tynzenella nexilis, lacto-N-biose complex
ComponentsFibronectin type III domain-containing protein
KeywordsHYDROLASE / Glycoside hydrolase / lacto-N-biosidase / lacto-N-biose complex
Function / homology
Function and homology information


metabolic process / hydrolase activity, acting on glycosyl bonds / membrane => GO:0016020
Similarity search - Function
Coagulation factors 5/8 type C domain (FA58C) profile. / Pectin lyase fold / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Pectin lyase fold/virulence factor / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III ...Coagulation factors 5/8 type C domain (FA58C) profile. / Pectin lyase fold / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Pectin lyase fold/virulence factor / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Fibronectin type III domain-containing protein
Similarity search - Component
Biological speciesTyzzerella nexilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsYamada, C. / Fushinobu, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16J09251 Japan
Japan Society for the Promotion of Science (JSPS)18K14388 Japan
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2022
Title: Crystal structures of glycoside hydrolase family 136 lacto-N-biosidases from monkey gut- and human adult gut bacteria.
Authors: Yamada, C. / Katayama, T. / Fushinobu, S.
History
DepositionAug 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibronectin type III domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2492
Polymers64,8651
Non-polymers3831
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint9 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.205, 71.782, 161.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Fibronectin type III domain-containing protein / Lacto-N-biosidase


Mass: 64865.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tyzzerella nexilis (bacteria) / Gene: DXA47_02055 / Plasmid: pET23b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A413JBB4
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M potassium formate, 20% (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-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 12, 2017
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→45.61 Å / Num. obs: 50268 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Net I/σ(I): 11.3
Reflection shellResolution: 1.92→1.96 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3314 / CC1/2: 0.814 / Rpim(I) all: 0.325 / Rrim(I) all: 0.726 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GQF

5gqf


Resolution: 1.92→45.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.094 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20949 2595 5.2 %RANDOM
Rwork0.16956 ---
obs0.17165 47615 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.644 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0 Å2-0 Å2
2---1.31 Å20 Å2
3---0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.92→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 26 400 4856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134557
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184040
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.6536198
X-RAY DIFFRACTIONr_angle_other_deg1.3871.5989334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.575569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.40525.709247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28415713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.093159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021049
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_it1.7612.1532279
X-RAY DIFFRACTIONr_mcbond_other1.7592.1532278
X-RAY DIFFRACTIONr_mcangle_it2.4113.2232847
X-RAY DIFFRACTIONr_mcangle_other2.4113.2232848
X-RAY DIFFRACTIONr_scbond_it2.5482.3462276
X-RAY DIFFRACTIONr_scbond_other2.5482.3462276
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.883.4213351
X-RAY DIFFRACTIONr_long_range_B_refined4.97525.4115117
X-RAY DIFFRACTIONr_long_range_B_other4.97525.4115118
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.966 Å
RfactorNum. reflection% reflection
Rfree0.312 201 -
Rwork0.258 3462 -
obs--99.38 %

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