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

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Basic information

Entry
Database: PDB / ID: 7qyp
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
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.659 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 28, 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)115,41012
Polymers114,7892
Non-polymers62110
Water12,683704
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)79.895, 79.895, 349.328
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 290 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: 0.97951 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: 1.659→79.89 Å / Num. obs: 135097 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.168 / Net I/σ(I): 6.9
Reflection shellResolution: 1.66→1.69 Å / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 6572 / CC1/2: 0.435 / % possible all: 99.21

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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: 1.659→78.005 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.357 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.122
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2727 6556 4.917 %
Rwork0.2218 126770 -
all0.224 --
obs-133326 98.77 %
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: 29.929 Å2
Baniso -1Baniso -2Baniso -3
1-0.764 Å20 Å20 Å2
2--0.764 Å20 Å2
3----1.529 Å2
Refinement stepCycle: LAST / Resolution: 1.659→78.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8046 0 40 704 8790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138268
X-RAY DIFFRACTIONr_bond_other_d0.0020.0147842
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.64511214
X-RAY DIFFRACTIONr_angle_other_deg1.3571.5818012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.16351044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12921.284436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.289151404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7141572
X-RAY DIFFRACTIONr_chiral_restr0.0790.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021920
X-RAY DIFFRACTIONr_nbd_refined0.1980.21447
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.27931
X-RAY DIFFRACTIONr_nbtor_refined0.1550.23918
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24146
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2679
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1050.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.25
X-RAY DIFFRACTIONr_nbd_other0.1760.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.25
X-RAY DIFFRACTIONr_mcbond_it7.1061.7284170
X-RAY DIFFRACTIONr_mcbond_other7.1061.7284169
X-RAY DIFFRACTIONr_mcangle_it6.7472.5625216
X-RAY DIFFRACTIONr_mcangle_other6.7472.5625217
X-RAY DIFFRACTIONr_scbond_it10.582.0834098
X-RAY DIFFRACTIONr_scbond_other10.5792.0834099
X-RAY DIFFRACTIONr_scangle_it10.7252.9465998
X-RAY DIFFRACTIONr_scangle_other10.7252.9475999
X-RAY DIFFRACTIONr_lrange_it11.08221.8069115
X-RAY DIFFRACTIONr_lrange_other11.13121.2868950
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.0516907
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.08890.05009
12BX-RAY DIFFRACTIONLocal ncs0.08890.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.659-1.7020.4044730.3969300X-RAY DIFFRACTION99.3999
1.702-1.7490.3774650.3619076X-RAY DIFFRACTION99.979
1.749-1.80.3374610.3288870X-RAY DIFFRACTION99.8929
1.8-1.8550.3334500.318633X-RAY DIFFRACTION99.8571
1.855-1.9160.3694420.3058302X-RAY DIFFRACTION99.5333
1.916-1.9830.3183640.2788121X-RAY DIFFRACTION99.5425
1.983-2.0580.3044140.2467784X-RAY DIFFRACTION99.4541
2.058-2.1420.3033810.2397488X-RAY DIFFRACTION99.3937
2.142-2.2370.2883650.2387170X-RAY DIFFRACTION98.8586
2.237-2.3460.3193460.2376897X-RAY DIFFRACTION98.6785
2.346-2.4730.2813430.2146478X-RAY DIFFRACTION98.4413
2.473-2.6230.3083210.2146152X-RAY DIFFRACTION97.7499
2.623-2.8040.3033120.2265746X-RAY DIFFRACTION97.3329
2.804-3.0290.2622780.2165365X-RAY DIFFRACTION96.7759
3.029-3.3180.2572640.2094964X-RAY DIFFRACTION96.618
3.318-3.710.2732510.2164475X-RAY DIFFRACTION97.063
3.71-4.2840.2181870.1784074X-RAY DIFFRACTION97.5504
4.284-5.2460.1812030.1433473X-RAY DIFFRACTION98.0267
5.246-7.4180.1811430.1512752X-RAY DIFFRACTION97.5076
7.418-78.0050.266930.1871650X-RAY DIFFRACTION98.4746
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)
10.8082-0.13490.06140.96280.26730.5405-0.0217-0.09490.07570.11450.00280.0339-0.00680.02460.01890.0334-0.00480.00280.0977-0.02770.01340.854116.001734.2084
20.99010.1325-0.25890.91280.12250.57250.0091-0.0253-0.0966-0.0163-0.0137-0.12550.13980.08090.00460.09190.08110.00380.10090.02430.040519.0152-17.12113.3773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA34 - 552
2X-RAY DIFFRACTION1ALLA601
3X-RAY DIFFRACTION1ALLA701
4X-RAY DIFFRACTION1ALLA801
5X-RAY DIFFRACTION1ALLA901
6X-RAY DIFFRACTION2ALLB34 - 552
7X-RAY DIFFRACTION2ALLB601
8X-RAY DIFFRACTION2ALLB701

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