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- PDB-4yw4: Streptococcus pneumoniae sialidase NanC -

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Basic information

Entry
Database: PDB / ID: 4yw4
TitleStreptococcus pneumoniae sialidase NanC
ComponentsNeuraminidase C
KeywordsHYDROLASE / Sialidase / Neuraminidase / NanC / CBM40
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / carbohydrate metabolic process
Similarity search - Function
BNR repeat / BNR/Asp-box repeat / Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase ...BNR repeat / BNR/Asp-box repeat / Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Neuraminidase C / :
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsOwen, C.D. / Lukacik, P. / Potter, J.A. / Walsh, M. / Taylor, G.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/F016778/1 United Kingdom
CitationJournal: To be published
Title: Crystal structure of a novel sialidase
Authors: Owen, C.D. / Lukacik, P. / Potter, J.A. / Walsh, M. / Taylor, G.L.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Data collection
Category: atom_site / diffrn_radiation_wavelength / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Neuraminidase C
B: Neuraminidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3316
Polymers147,9572
Non-polymers3744
Water7,026390
1
A: Neuraminidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1663
Polymers73,9791
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuraminidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1663
Polymers73,9791
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.697, 74.770, 113.110
Angle α, β, γ (deg.)90.000, 95.710, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 83 - 741 / Label seq-ID: 1 - 659

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Neuraminidase C


Mass: 73978.609 Da / Num. of mol.: 2 / Fragment: unp residues 83-740
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: G54 / Gene: nanC, SPG_1219 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B5E561, UniProt: A0A182DW00*PLUS, exo-alpha-sialidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 16% PEG8000, 20% glycerol, 40mM monopotassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.2→59.709 Å / Num. all: 83261 / Num. obs: 83261 / % possible obs: 98.9 % / Redundancy: 2.7 % / Rpim(I) all: 0.064 / Rrim(I) all: 0.11 / Rsym value: 0.089 / Net I/av σ(I): 6.123 / Net I/σ(I): 7.6 / Num. measured all: 224169
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.262.70.352.11648361900.2580.352.899.4
2.26-2.322.70.3122.31602560000.230.3123.199.4
2.32-2.392.70.272.71560958110.1980.273.599.2
2.39-2.462.70.2323.11519856750.170.232499.4
2.46-2.542.70.2213.31471254810.1610.2214.299.2
2.54-2.632.70.1913.41422553100.140.1914.899.2
2.63-2.732.70.1624.41379451440.1180.1625.599.2
2.73-2.842.70.1414.91333449380.1020.1416.399.2
2.84-2.972.70.1195.71275247240.0860.1197.399.1
2.97-3.112.70.0956.91228845270.0680.0958.598.8
3.11-3.282.70.0847.41157642840.060.0849.698.7
3.28-3.482.70.0777.61104140530.0550.07710.998.7
3.48-3.722.70.0718.31034938250.0510.07111.998.8
3.72-4.022.70.0678.5963535530.0470.06712.998.5
4.02-4.42.70.0578.9896632870.0410.05713.698.4
4.4-4.922.70.04811.2798929540.0350.04814.698.1
4.92-5.682.70.0539.3713426140.0380.05314.197.7
5.68-6.962.70.05410.5596222030.0380.05413.598
6.96-9.842.70.04512461217180.0320.04514.597.2
9.84-59.7092.60.04211.524859700.0310.04215.696.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VW0

2vw0


Resolution: 2.2→59.709 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2155 / WRfactor Rwork: 0.1824 / FOM work R set: 0.8361 / SU B: 11.564 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2258 / SU Rfree: 0.1785 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 4158 5 %RANDOM
Rwork0.1818 ---
obs0.1834 79085 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.98 Å2 / Biso mean: 36.645 Å2 / Biso min: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å22.35 Å2
2---2.25 Å20 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 2.2→59.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10444 0 22 390 10856
Biso mean--29.91 30.46 -
Num. residues----1318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0210720
X-RAY DIFFRACTIONr_bond_other_d0.0050.029978
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.94614532
X-RAY DIFFRACTIONr_angle_other_deg1.14322994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.42451320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86624.762504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.588151816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6621546
X-RAY DIFFRACTIONr_chiral_restr0.0910.21576
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212272
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022522
X-RAY DIFFRACTIONr_mcbond_it2.1481.1695280
X-RAY DIFFRACTIONr_mcbond_other2.1481.1695279
X-RAY DIFFRACTIONr_mcangle_it3.1551.7456600
Refine LS restraints NCS

Ens-ID: 1 / Number: 80746 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 272 -
Rwork0.256 5915 -
all-6187 -
obs--99.37 %
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)
10.8615-0.41720.10220.84110.00360.95810.05160.0094-0.0568-0.00590.00710.1247-0.0431-0.0579-0.05870.1814-0.0306-0.10770.15530.03660.0927-24.26116.72-5.173
20.37560.4493-0.61521.6913-1.37452.10780.0236-0.0014-0.01780.2941-0.0065-0.0371-0.0950.0507-0.01710.26510.0299-0.11640.17150.00760.0664-20.576-7.875-57.407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A83 - 742
2X-RAY DIFFRACTION2B83 - 741

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