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- PDB-7qz3: The structure of T. forsythia NanH -

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Basic information

Entry
Database: PDB / ID: 7qz3
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: 1.97 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 30, 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)115,2664
Polymers114,7892
Non-polymers4772
Water7,656425
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint7 kcal/mol
Surface area35610 Å2
Unit cell
Length a, b, c (Å)79.740, 79.740, 349.500
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.42 Å3/Da / Density % sol: 49.17 % / Description: bipyramid
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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.97→77.863 Å / Num. obs: 80616 / % possible obs: 99.4 % / Redundancy: 3.81 % / CC1/2: 1 / Net I/σ(I): 21.8
Reflection shellResolution: 1.97→2.01 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4386 / CC1/2: 0.472

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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: 1.97→77.863 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 13.561 / SU ML: 0.181 / Cross valid method: FREE R-VALUE / ESU R: 0.206 / ESU R Free: 0.178
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2662 3899 4.837 %
Rwork0.2304 76716 -
all0.232 --
obs-80615 99.314 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.851 Å2
Baniso -1Baniso -2Baniso -3
1-2.005 Å20 Å20 Å2
2--2.005 Å20 Å2
3----4.01 Å2
Refinement stepCycle: LAST / Resolution: 1.97→77.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8046 0 30 425 8501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138239
X-RAY DIFFRACTIONr_bond_other_d0.0010.0147791
X-RAY DIFFRACTIONr_angle_refined_deg1.351.64411190
X-RAY DIFFRACTIONr_angle_other_deg1.171.5817905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.11151038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34421.264435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.743151397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9781572
X-RAY DIFFRACTIONr_chiral_restr0.0540.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021912
X-RAY DIFFRACTIONr_nbd_refined0.1810.21416
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.27845
X-RAY DIFFRACTIONr_nbtor_refined0.1470.23894
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.23995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2494
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0740.25
X-RAY DIFFRACTIONr_nbd_other0.1620.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2320.25
X-RAY DIFFRACTIONr_mcbond_it1.192.9594155
X-RAY DIFFRACTIONr_mcbond_other1.192.9584154
X-RAY DIFFRACTIONr_mcangle_it1.7464.4335192
X-RAY DIFFRACTIONr_mcangle_other1.7464.4345193
X-RAY DIFFRACTIONr_scbond_it1.2193.0964084
X-RAY DIFFRACTIONr_scbond_other1.2153.0964082
X-RAY DIFFRACTIONr_scangle_it1.8794.5965998
X-RAY DIFFRACTIONr_scangle_other1.8794.5975999
X-RAY DIFFRACTIONr_lrange_it4.07134.7458875
X-RAY DIFFRACTIONr_lrange_other4.04334.5318812
X-RAY DIFFRACTIONr_ncsr_local_group_10.0770.0517009
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.077220.0501
12BX-RAY DIFFRACTIONLocal ncs0.077220.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.0210.382920.3825429X-RAY DIFFRACTION97.0483
2.021-2.0770.3642490.3535345X-RAY DIFFRACTION97.4055
2.077-2.1370.3862410.3275304X-RAY DIFFRACTION99.3728
2.137-2.2030.3552470.2975181X-RAY DIFFRACTION99.505
2.203-2.2750.3642510.3285014X-RAY DIFFRACTION99.5274
2.275-2.3550.3362260.2664872X-RAY DIFFRACTION99.6871
2.355-2.4430.272680.2434646X-RAY DIFFRACTION99.6957
2.443-2.5430.2932370.2364512X-RAY DIFFRACTION99.6224
2.543-2.6560.3062300.2574355X-RAY DIFFRACTION99.6306
2.656-2.7860.272240.244118X-RAY DIFFRACTION99.7244
2.786-2.9370.2752150.2363982X-RAY DIFFRACTION99.7386
2.937-3.1150.2992000.243756X-RAY DIFFRACTION99.773
3.115-3.330.2871740.2333585X-RAY DIFFRACTION99.7082
3.33-3.5970.251600.2353328X-RAY DIFFRACTION99.8283
3.597-3.940.2291660.223071X-RAY DIFFRACTION99.815
3.94-4.4050.2441320.192818X-RAY DIFFRACTION99.7296
4.405-5.0860.2151370.1732495X-RAY DIFFRACTION99.8104
5.086-6.2290.2980.1882176X-RAY DIFFRACTION99.956
6.229-8.8070.223960.1831706X-RAY DIFFRACTION99.9445
8.807-77.8630.218560.1821023X-RAY DIFFRACTION98.9908
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)
10.9194-0.14420.06561.22250.65831.372-0.0898-0.15410.13530.20080.01620.0398-0.01570.15860.07360.0606-0.0074-0.00380.0563-0.01880.03890.825415.999634.3176
21.2507-0.0184-0.35090.88410.18590.6580.0117-0.0128-0.13320.1315-0.037-0.13480.25790.26070.02530.12520.1145-0.01150.15110.04710.098618.9481-17.221813.2988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA34 - 552
2X-RAY DIFFRACTION2ALLB34 - 552

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