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

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Basic information

Entry
Database: PDB / ID: 7qxo
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
Chem-GHD / exo-alpha-sialidase
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 26, 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
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-12 kcal/mol
Surface area35950 Å2
Unit cell
Length a, b, c (Å)79.868, 79.868, 349.449
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-GHD / (2~{R},4~{S},5~{S},6~{S})-5-acetamido-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]-2-[[(2~{R},3~{R},4~{S},5~{R},6~{S})-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{R},5~{R})-1,2,4,5-tetrakis(oxidanyl)-6-oxidanylidene-hexan-3-yl]oxy-oxan-2-yl]methoxy]oxane-2-carboxylic acid


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.: 393 / 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: 49.37 % / Description: bipyramid
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: 1.9→72.64 Å / Num. obs: 90670 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 0.964 / Rmerge(I) obs: 0.141 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 2.525 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4317 / CC1/2: 0.668 / % possible all: 98.29

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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: 1.9→72.64 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.923 / SU B: 13.034 / SU ML: 0.183 / Cross valid method: FREE R-VALUE / ESU R: 0.197 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2903 4483 4.954 %
Rwork0.2518 86014 -
all0.254 --
obs-90497 99.89 %
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: 43.051 Å2
Baniso -1Baniso -2Baniso -3
1-1.763 Å2-0 Å20 Å2
2--1.763 Å20 Å2
3----3.527 Å2
Refinement stepCycle: LAST / Resolution: 1.9→72.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8044 0 86 393 8523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138295
X-RAY DIFFRACTIONr_bond_other_d0.0010.0147816
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.64611275
X-RAY DIFFRACTIONr_angle_other_deg1.1771.5817975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.95851038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22821.193436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.527151397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7571572
X-RAY DIFFRACTIONr_chiral_restr0.0560.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029364
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021916
X-RAY DIFFRACTIONr_nbd_refined0.180.21391
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.27692
X-RAY DIFFRACTIONr_nbtor_refined0.1460.23891
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.24043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2448
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1060.24
X-RAY DIFFRACTIONr_nbd_other0.1580.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.140.23
X-RAY DIFFRACTIONr_mcbond_it0.922.8474155
X-RAY DIFFRACTIONr_mcbond_other0.922.8474154
X-RAY DIFFRACTIONr_mcangle_it1.4054.2665192
X-RAY DIFFRACTIONr_mcangle_other1.4054.2665193
X-RAY DIFFRACTIONr_scbond_it0.9882.9984140
X-RAY DIFFRACTIONr_scbond_other0.9882.9994141
X-RAY DIFFRACTIONr_scangle_it1.5714.4586083
X-RAY DIFFRACTIONr_scangle_other1.5714.4586084
X-RAY DIFFRACTIONr_lrange_it4.74333.58829
X-RAY DIFFRACTIONr_lrange_other4.82633.3448777
X-RAY DIFFRACTIONr_ncsr_local_group_10.0840.0516695
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.084140.05009
12BX-RAY DIFFRACTIONLocal ncs0.084140.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.4072980.3966224X-RAY DIFFRACTION98.7882
1.949-2.0020.333210.3416066X-RAY DIFFRACTION99.9687
2.002-2.060.3243180.3265914X-RAY DIFFRACTION99.9679
2.06-2.1240.3563100.3125774X-RAY DIFFRACTION99.9671
2.124-2.1930.2912660.2885596X-RAY DIFFRACTION99.9659
2.193-2.270.3273130.3355414X-RAY DIFFRACTION99.9476
2.27-2.3560.3322840.2865269X-RAY DIFFRACTION99.964
2.356-2.4520.3372730.2815019X-RAY DIFFRACTION100
2.452-2.5610.3052410.2654875X-RAY DIFFRACTION100
2.561-2.6860.3432470.2674660X-RAY DIFFRACTION99.9796
2.686-2.8310.3412430.2584425X-RAY DIFFRACTION99.9786
2.831-3.0030.3181960.2554227X-RAY DIFFRACTION100
3.003-3.2110.3041990.2563995X-RAY DIFFRACTION99.9523
3.211-3.4680.3112010.2563728X-RAY DIFFRACTION100
3.468-3.7990.2871590.2463459X-RAY DIFFRACTION100
3.799-4.2470.261560.2243132X-RAY DIFFRACTION100
4.247-4.9040.2291510.22794X-RAY DIFFRACTION100
4.904-6.0060.2491330.2062396X-RAY DIFFRACTION100
6.006-8.4920.2241080.1851901X-RAY DIFFRACTION100
8.492-72.640.249660.2321146X-RAY DIFFRACTION99.7531
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)
10.9887-0.17240.03661.28270.77121.4498-0.106-0.16410.15490.1810.02640.03920.00680.17940.07960.0408-0.0002-0.0110.0633-0.01940.02890.841615.892934.234
21.41120.0021-0.35320.88920.28870.71640.014-0.0417-0.11250.0894-0.0267-0.13960.27530.26770.01270.12830.1222-0.00330.1630.05910.084318.9002-17.104613.2693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA34 - 552
2X-RAY DIFFRACTION2ALLB34 - 552

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