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Basic information

Entry
Database: PDB / ID: 5f9t
TitleCrystal Structure of Streptococcus pneumoniae NanC, covalent complex with a fluorinated Neu5Ac derivative
ComponentsNeuraminidase C
KeywordsHYDROLASE / Sialidase / Neuraminidase / covalent intermediate / CBM40
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
BNR repeat / BNR/Asp-box repeat / Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / 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 / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / 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
Chem-FSI / Chem-SFJ / exo-alpha-sialidase / exo-alpha-sialidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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: J.Biol.Chem. / Year: 2015
Title: Streptococcus pneumoniae NanC: STRUCTURAL INSIGHTS INTO THE SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODUCES A SIALIDASE INHIBITOR.
Authors: Owen, C.D. / Lukacik, P. / Potter, J.A. / Sleator, O. / Taylor, G.L. / Walsh, M.A.
History
DepositionDec 10, 2015Deposition site: RCSB / Processing site: PDBE
SupersessionDec 23, 2015ID: 4YW0
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jun 30, 2021Group: Database references / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _entity.pdbx_ec ..._chem_comp.pdbx_synonyms / _entity.pdbx_ec / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 2.2Jan 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
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)149,3627
Polymers147,9572
Non-polymers1,4055
Water9,962553
1
A: Neuraminidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6353
Polymers73,9791
Non-polymers6572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuraminidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7274
Polymers73,9791
Non-polymers7493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.236, 74.843, 113.352
Angle α, β, γ (deg.)90.000, 96.310, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / 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: _ / 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 / Putative neuraminidase


Mass: 73978.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1326 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H2UQE4, UniProt: A0A0B7LH44*PLUS, exo-alpha-sialidase
#2: Sugar ChemComp-FSI / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 5-(acetylamino)-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 3-FLUOROSIALIC ACID / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulosonic acid / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-L-manno-non-2-ulosonic acid / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-manno-non-2-ulosonic acid


Type: D-saccharide, beta linking / Mass: 327.260 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C11H18FNO9
IdentifierTypeProgram
b-D-Neup5Ac3fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-SFJ / (2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid / (2R,3R,4R,5R,6R)-5-(acetylamino)-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxy lic acid / 2,3-difluoro-sialic acid / 5-acetamido-2,3-difluoro-3-hydroxy-6-[1,2,3-trihydroxypropyl]oxane-2-carboxylic acid


Type: D-saccharide / Mass: 329.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17F2NO8
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 16% PEG8000, 20% glycerol, 40mM monopotassium phosphate, 10% sugar free Irn Bru

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 102205 / % possible obs: 97.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.107 / Χ2: 2.014 / Net I/av σ(I): 15.966 / Net I/σ(I): 9.1 / Num. measured all: 360436
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.05-2.092.80.57639301.94475.1
2.09-2.1230.55543972.07384.7
2.12-2.163.30.52149782.05396
2.16-2.213.50.52852052.12199.9
2.21-2.263.50.50651932.06100
2.26-2.313.60.43952021.99799.9
2.31-2.373.60.41551712.05100
2.37-2.433.60.37552282.017100
2.43-2.53.60.34752241.997100
2.5-2.583.50.3351852.078100
2.58-2.673.50.27852252.062100
2.67-2.783.50.23752121.99100
2.78-2.913.50.252102.06399.9
2.91-3.063.50.14952122.10399.9
3.06-3.253.70.10652482.106100
3.25-3.53.80.07352372.233100
3.5-3.863.80.05652282.18699.9
3.86-4.413.70.04552741.885100
4.41-5.553.70.03652821.61299.9
5.55-303.60.03453641.65999.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å23.63 Å
Translation3.5 Å23.63 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vw2

2vw2


Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.1696 / FOM work R set: 0.8067 / SU B: 9.551 / SU ML: 0.129 / SU R Cruickshank DPI: 0.1914 / SU Rfree: 0.1673 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 5098 5 %RANDOM
Rwork0.1976 ---
obs0.1995 96897 97.37 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 174.14 Å2 / Biso mean: 33.251 Å2 / Biso min: 12.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0.1 Å2
2--0.25 Å20 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10444 0 92 553 11089
Biso mean--31.56 30.3 -
Num. residues----1318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0210796
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210023
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.95514650
X-RAY DIFFRACTIONr_angle_other_deg1.094323113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3251320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2424.751503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.524151819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.651546
X-RAY DIFFRACTIONr_chiral_restr0.0810.21605
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212305
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022523
X-RAY DIFFRACTIONr_mcbond_it5.3071.4125280
X-RAY DIFFRACTIONr_mcbond_other5.3071.4125279
X-RAY DIFFRACTIONr_mcangle_it5.72.0866600
Refine LS restraints NCS

Ens-ID: 1 / Number: 82570 / 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: 2.051→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 313 -
Rwork0.259 5523 -
all-5836 -
obs--76.33 %
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)
11.6292-0.57620.08951.6728-0.06571.34980.05070.0232-0.1843-0.02610.01350.09410.18250.12-0.06430.12980.0189-0.07430.043-0.01220.0888137.4637-4.39346.2688
21.4015-0.47330.07511.4814-0.20441.6287-0.0025-0.02360.0955-0.00770.05710.0434-0.1268-0.0204-0.05450.1172-0.0301-0.03250.0470.00510.0937122.145625.020954.1905
33.4352-1.0227-0.01771.6098-0.39011.8676-0.1123-0.26440.24830.21070.16710.2609-0.2983-0.317-0.05470.31350.08690.03030.179-0.03680.1154111.078638.870873.872
45.721-4.5574.921911.6756-4.46696.04250.0530.1942-0.3223-0.3589-0.1942-1.92980.23311.57470.14120.44880.12030.03841.12130.20390.6596132.86369.696571.1453
50.9359-0.30450.18630.78680.03951.07140.04750.0427-0.0252-0.05890.00710.2255-0.1085-0.1946-0.05450.0956-0.0019-0.040.06320.04650.1282109.343123.511946.3694
61.05520.5049-0.52252.5147-0.62512.2985-0.12380.0315-0.0870.00880.07620.14210.4597-0.21830.04760.3706-0.05470.03110.07750.01250.1448111.7002-30.25288.6595
70.98460.5456-0.22992.3059-0.49972.43140.04180.03450.06390.1790.01210.0894-0.1864-0.0742-0.05380.14880.0199-0.0210.06660.02210.0901120.03830.1654-4.2601
82.9966-0.91780.16742.8472-1.60974.33770.08270.0447-0.04350.0098-0.0028-0.178-0.12090.1603-0.07990.1725-0.01040.01760.09690.04140.0593128.179515.84-27.7194
92.21511.0422-0.5654.0384-2.27223.4729-0.01580.20760.0131-0.30320.2230.19810.0719-0.4438-0.20720.10910.03-0.04310.22610.04830.0711112.04734.3018-22.2778
100.5540.2395-0.23791.2204-0.83891.96970.0796-0.103-0.02260.3217-0.2397-0.2937-0.28770.48570.16020.2012-0.0703-0.09090.14880.0490.1176136.00260.88442.3122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A83 - 273
2X-RAY DIFFRACTION2A274 - 395
3X-RAY DIFFRACTION3A396 - 469
4X-RAY DIFFRACTION4A470 - 474
5X-RAY DIFFRACTION5A475 - 741
6X-RAY DIFFRACTION6B83 - 276
7X-RAY DIFFRACTION7B277 - 396
8X-RAY DIFFRACTION8B397 - 444
9X-RAY DIFFRACTION9B445 - 493
10X-RAY DIFFRACTION10B494 - 741

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