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- PDB-7qy9: The structure of T.forsythia NanH with oseltamivir -

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Basic information

Entry
Database: PDB / ID: 7qy9
TitleThe structure of T.forsythia NanH with oseltamivir
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
Chem-G39 / exo-alpha-sialidase
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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)115,3584
Polymers114,7892
Non-polymers5692
Water5,405300
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.501, 79.501, 348.851
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: 57394.680 Da / Num. of mol.: 2
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-G39 / (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid / Oseltamivir carboxylate


Mass: 284.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H24N2O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.4 Å3/Da / Density % sol: 48.8 % / Description: bipyramid
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 7% PEG6000 100 mM HEPES buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.92→79.5 Å / Num. obs: 87048 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.998 / Net I/σ(I): 10.6
Reflection shellResolution: 1.92→1.95 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4278 / CC1/2: 0.623

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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: 1.92→77.634 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.882 / SU B: 19.933 / SU ML: 0.268 / Cross valid method: FREE R-VALUE / ESU R: 0.268 / ESU R Free: 0.224
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3457 4147 5.015 %
Rwork0.3128 78537 -
all0.315 --
obs-82684 95.144 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.123 Å2
Baniso -1Baniso -2Baniso -3
1--0.343 Å2-0 Å2-0 Å2
2---0.343 Å2-0 Å2
3---0.685 Å2
Refinement stepCycle: LAST / Resolution: 1.92→77.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8046 0 40 300 8386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0147801
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.64311193
X-RAY DIFFRACTIONr_angle_other_deg1.1691.5817918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76251036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17921.111441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.053151396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9131572
X-RAY DIFFRACTIONr_chiral_restr0.0510.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021914
X-RAY DIFFRACTIONr_nbd_refined0.180.21375
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.27804
X-RAY DIFFRACTIONr_nbtor_refined0.1470.23847
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.23948
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2371
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0920.27
X-RAY DIFFRACTIONr_nbd_other0.1620.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.070.22
X-RAY DIFFRACTIONr_mcbond_it0.6491.5464150
X-RAY DIFFRACTIONr_mcbond_other0.6491.5454149
X-RAY DIFFRACTIONr_mcangle_it1.1622.3155184
X-RAY DIFFRACTIONr_mcangle_other1.1622.3165185
X-RAY DIFFRACTIONr_scbond_it0.4761.6034092
X-RAY DIFFRACTIONr_scbond_other0.4761.6034093
X-RAY DIFFRACTIONr_scangle_it0.8712.3816009
X-RAY DIFFRACTIONr_scangle_other0.8712.3816010
X-RAY DIFFRACTIONr_lrange_it3.97417.7748680
X-RAY DIFFRACTIONr_lrange_other3.95417.6658648
X-RAY DIFFRACTIONr_ncsr_local_group_10.080.0516669
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.080360.05009
12BX-RAY DIFFRACTIONLocal ncs0.080360.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.5132640.475055X-RAY DIFFRACTION84.3349
1.97-2.0240.4562900.4145813X-RAY DIFFRACTION98.9462
2.024-2.0820.462950.4355608X-RAY DIFFRACTION98.3178
2.082-2.1460.4042960.3875456X-RAY DIFFRACTION98.7298
2.146-2.2170.3812820.3765299X-RAY DIFFRACTION98.989
2.217-2.2950.681930.6743712X-RAY DIFFRACTION71.1942
2.295-2.3810.3872410.3624957X-RAY DIFFRACTION98.4656
2.381-2.4780.3942650.3434744X-RAY DIFFRACTION98.0811
2.478-2.5890.3622660.334541X-RAY DIFFRACTION98.1421
2.589-2.7150.3662170.3414358X-RAY DIFFRACTION97.5272
2.715-2.8620.4082100.3324209X-RAY DIFFRACTION97.7222
2.862-3.0350.3562110.3083907X-RAY DIFFRACTION97.3062
3.035-3.2450.361880.2953706X-RAY DIFFRACTION97.277
3.245-3.5050.3171860.2843470X-RAY DIFFRACTION97.234
3.505-3.840.3431680.2993092X-RAY DIFFRACTION93.894
3.84-4.2930.2961420.2442901X-RAY DIFFRACTION96.389
4.293-4.9570.2121440.2012628X-RAY DIFFRACTION97.5369
4.957-6.070.2421310.22217X-RAY DIFFRACTION97.105
6.07-8.5830.243920.1931789X-RAY DIFFRACTION97.7651
8.583-77.6340.199660.2171075X-RAY DIFFRACTION97.4381
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)
10.1109-0.1395-0.23090.39660.71281.3184-0.1837-0.00090.02370.08450.05790.09650.04910.20620.12580.4523-0.0488-0.02240.262-0.02190.13020.751916.030834.2282
20.3734-0.0253-0.18970.49360.150.3252-0.0792-0.00220.04980.2096-0.00590.05090.27690.28140.08510.41110.18540.03420.46050.12050.049718.9443-17.129613.2282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA34 - 552
2X-RAY DIFFRACTION2ALLB34 - 552

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