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- PDB-7qy8: The structure of T. forsythia NanH -

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Basic information

Entry
Database: PDB / ID: 7qy8
TitleThe structure of T. forsythia NanH
ComponentsBNR/Asp-box repeat protein
KeywordsHYDROLASE / Sialidase
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
Sialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
3-sialyllactose / exo-alpha-sialidase
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsRafferty, J. / Stafford, G. / Satur, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Biochem.J. / Year: 2022
Title: Structural and functional characterisation of a stable, broad-specificity multimeric sialidase from the oral pathogen Tannerella forsythia.
Authors: Satur, M.J. / Urbanowicz, P.A. / Spencer, D.I.R. / Rafferty, J. / Stafford, G.P.
History
DepositionJan 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BNR/Asp-box repeat protein
B: BNR/Asp-box repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9684
Polymers114,7012
Non-polymers1,2672
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-12 kcal/mol
Surface area35820 Å2
Unit cell
Length a, b, c (Å)80.059, 80.059, 349.789
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 34 - 552 / Label seq-ID: 1 - 519

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein BNR/Asp-box repeat protein


Mass: 57350.672 Da / Num. of mol.: 2 / Mutation: D237A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria)
Strain: ATCC 43037 / JCM 10827 / CCUG 33226 / KCTC 5666 / FDC 338
Gene: BFO_2207 / Production host: Escherichia coli (E. coli) / References: UniProt: G8UIQ1
#2: Chemical ChemComp-I2K / 3-sialyllactose


Mass: 633.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H39NO19 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 7% PEG6000 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 2.06→72.901 Å / Num. obs: 71921 / % possible obs: 100 % / Redundancy: 25.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.158 / Net I/σ(I): 14.8
Reflection shellResolution: 2.06→2.1 Å / Rmerge(I) obs: 2.964 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3491 / CC1/2: 0.797

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bbw

4bbw


Resolution: 2.06→72.901 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.931 / SU B: 16.71 / SU ML: 0.207 / Cross valid method: FREE R-VALUE / ESU R: 0.255 / ESU R Free: 0.206
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2786 3626 5.067 %
Rwork0.2448 67938 -
all0.246 --
obs-71564 99.695 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.091 Å2
Baniso -1Baniso -2Baniso -3
1-1.909 Å20 Å20 Å2
2--1.909 Å20 Å2
3----3.818 Å2
Refinement stepCycle: LAST / Resolution: 2.06→72.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8019 0 86 325 8430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138270
X-RAY DIFFRACTIONr_bond_other_d0.0010.0147772
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.64611247
X-RAY DIFFRACTIONr_angle_other_deg1.1251.57917865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.83251038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52621.204432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.597151379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1641571
X-RAY DIFFRACTIONr_chiral_restr0.0470.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021911
X-RAY DIFFRACTIONr_nbd_refined0.1760.21409
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.27744
X-RAY DIFFRACTIONr_nbtor_refined0.1450.23896
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.24044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2440
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0380.24
X-RAY DIFFRACTIONr_nbd_other0.1620.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.25
X-RAY DIFFRACTIONr_mcbond_it0.9893.3634155
X-RAY DIFFRACTIONr_mcbond_other0.9893.3634154
X-RAY DIFFRACTIONr_mcangle_it1.5465.0415192
X-RAY DIFFRACTIONr_mcangle_other1.5455.0425193
X-RAY DIFFRACTIONr_scbond_it1.1153.5524115
X-RAY DIFFRACTIONr_scbond_other1.1153.5534116
X-RAY DIFFRACTIONr_scangle_it1.815.2866055
X-RAY DIFFRACTIONr_scangle_other1.8095.2876056
X-RAY DIFFRACTIONr_lrange_it5.61839.9898837
X-RAY DIFFRACTIONr_lrange_other5.56239.8258795
X-RAY DIFFRACTIONr_ncsr_local_group_10.0830.0516750
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.083390.0501
12BX-RAY DIFFRACTIONLocal ncs0.083390.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.1130.3822470.3614935X-RAY DIFFRACTION99.9614
2.113-2.1710.3642570.3394839X-RAY DIFFRACTION100
2.171-2.2340.3912420.3414629X-RAY DIFFRACTION98.7632
2.234-2.3030.6232470.564417X-RAY DIFFRACTION97.106
2.303-2.3780.3172350.2954407X-RAY DIFFRACTION100
2.378-2.4620.3022360.2744307X-RAY DIFFRACTION99.934
2.462-2.5550.341950.2594171X-RAY DIFFRACTION100
2.555-2.6590.3322040.274007X-RAY DIFFRACTION100
2.659-2.7770.3262180.2613846X-RAY DIFFRACTION99.9754
2.777-2.9130.3172310.2593644X-RAY DIFFRACTION100
2.913-3.0710.2561870.2423540X-RAY DIFFRACTION100
3.071-3.2570.2931790.2473312X-RAY DIFFRACTION100
3.257-3.4820.2751890.2413145X-RAY DIFFRACTION100
3.482-3.7610.2681490.2512935X-RAY DIFFRACTION99.7735
3.761-4.1190.2591430.2132724X-RAY DIFFRACTION100
4.119-4.6060.1971230.1862498X-RAY DIFFRACTION100
4.606-5.3180.2091340.1842219X-RAY DIFFRACTION100
5.318-6.5130.261900.1891910X-RAY DIFFRACTION100
6.513-9.2090.191790.1831522X-RAY DIFFRACTION100
9.209-72.9010.208410.212932X-RAY DIFFRACTION99.3871
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8746-0.2521-0.06291.14250.57591.0802-0.0484-0.18850.13010.1406-0.00840.0495-0.00220.14710.05680.0279-0.0233-0.00090.1545-0.04640.04220.75415.895334.2647
21.0304-0.0024-0.25080.95640.26510.64070.0306-0.1146-0.09820.0354-0.0568-0.17180.25230.29190.02620.13350.13750.00090.24570.09610.10919.1637-17.048613.2945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA34 - 552
2X-RAY DIFFRACTION2ALLB34 - 552

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