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- PDB-4yw2: Crystal Structure of Streptococcus pneumoniae NanC, complex 6'SL -

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Basic information

Entry
Database: PDB / ID: 4yw2
TitleCrystal Structure of Streptococcus pneumoniae NanC, complex 6'SL
ComponentsNeuraminidase C
KeywordsHYDROLASE / Sialidase / Neuraminidase / 6'SL / 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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / exo-alpha-sialidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 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: 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
DepositionMar 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Aug 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_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Jun 30, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_src_gen / pdbx_nonpoly_scheme / refine / refine_hist / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
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 / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _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 / _pdbx_nonpoly_scheme.auth_seq_num / _refine.ls_d_res_low / _refine_hist.d_res_low / _struct_conn.pdbx_value_order / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 3.1Jan 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)149,56411
Polymers147,9572
Non-polymers1,6079
Water15,673870
1
A: Neuraminidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8356
Polymers73,9791
Non-polymers8575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuraminidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7295
Polymers73,9791
Non-polymers7514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.646, 74.906, 113.000
Angle α, β, γ (deg.)90.000, 96.210, 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

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Neuraminidase C / Putative neuraminidase


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 serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1326,nanC / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2UQE4, exo-alpha-sialidase
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 877 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 870 / 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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 16% PEG8000, 20% glycerol, 40mM monopotassium phosphate

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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 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 109231 / % possible obs: 96.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.109 / Χ2: 2.247 / Net I/av σ(I): 18.391 / Net I/σ(I): 9.8 / Num. measured all: 402378
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.033.60.47651162.09491.3
2.03-2.073.70.40853442.12994.7
2.07-2.113.70.36953442.13795.3
2.11-2.153.70.32353392.15895
2.15-2.23.70.353792.14695.2
2.2-2.253.70.29553842.10296.2
2.25-2.313.70.28454042.10195.9
2.31-2.373.70.26354002.11796.1
2.37-2.443.70.24554382.17696.4
2.44-2.523.70.22954312.12296.8
2.52-2.613.70.21654682.11697
2.61-2.713.60.18554892.14597.2
2.71-2.843.60.16754742.2397.2
2.84-2.993.60.13555052.2797.2
2.99-3.173.70.10655432.35398.3
3.17-3.423.80.07855482.60498
3.42-3.763.80.06456292.88598.7
3.76-4.313.70.05455942.55498.8
4.31-5.423.60.04456572.29398.9
5.42-303.60.04257452.12898.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å22.77 Å
Translation3.5 Å22.77 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vw0

2vw0


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.1796 / WRfactor Rwork: 0.1557 / FOM work R set: 0.865 / SU B: 6.174 / SU ML: 0.091 / SU R Cruickshank DPI: 0.1644 / SU Rfree: 0.1432 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 5435 5 %RANDOM
Rwork0.1797 ---
obs0.1812 103624 96.43 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 87.31 Å2 / Biso mean: 23.034 Å2 / Biso min: 8.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20.03 Å2
2--0.01 Å20 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10444 0 105 870 11419
Biso mean--35.94 26.93 -
Num. residues----1318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0210793
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210037
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.95414627
X-RAY DIFFRACTIONr_angle_other_deg1.127323135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.43551318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24724.751503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.029151815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8311546
X-RAY DIFFRACTIONr_chiral_restr0.0880.21599
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212274
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022522
X-RAY DIFFRACTIONr_mcbond_it1.1391.1735275
X-RAY DIFFRACTIONr_mcbond_other1.1391.1725274
X-RAY DIFFRACTIONr_mcangle_it1.7561.7516592
Refine LS restraints NCS

Ens-ID: 1 / Number: 82810 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 372 -
Rwork0.204 7309 -
all-7681 -
obs--92.05 %
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)
11.6083-0.68880.21471.419-0.07450.909-0.0147-0.0432-0.1150.02120.0470.08970.06380.0192-0.03220.02820.0038-0.02970.01080.00450.049937.642-4.29846.197
20.9497-0.22280.21150.93310.12291.6329-0.0020.03910.0234-0.0270.02830.0256-0.12230.0311-0.02640.0202-0.0113-0.01810.01650.01360.045122.50225.24753.278
33.9428-1.14110.31911.70220.35291.7279-0.0967-0.25740.13480.08180.00180.2159-0.2543-0.25260.09480.11270.02060.00970.1223-0.01260.062813.45336.23173.432
40.6092-0.04090.37790.64430.19971.13320.00830.01130.0206-0.1137-0.03250.1478-0.1165-0.15320.02420.03380.0113-0.03860.04980.02760.08828.53423.5945.255
51.26950.5678-0.23511.931-0.08521.0548-0.03490.0269-0.06880.0178-0.00490.06640.1483-0.06330.03970.1138-0.02020.00220.02590.00830.065611.219-30.4488.603
61.01990.51970.02571.3456-0.18271.66850.0110.05140.0650.03390.02590.0647-0.0877-0.042-0.03690.02560.0056-0.01030.02450.03110.055319.7080.176-4.204
73.1922-0.2077-0.08953.1949-2.06383.91750.02310.0174-0.05490.0945-0.0561-0.043-0.02650.14840.03290.06240.00190.01050.05990.0220.043625.94715.261-26.459
80.63210.02970.07030.6799-0.44021.23830.04420.00060.03660.0746-0.0904-0.0964-0.11030.2160.04630.0426-0.0248-0.0150.05710.01170.067132.6211.07-0.897
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A83 - 273
2X-RAY DIFFRACTION2A274 - 389
3X-RAY DIFFRACTION3A390 - 483
4X-RAY DIFFRACTION4A484 - 741
5X-RAY DIFFRACTION5B83 - 276
6X-RAY DIFFRACTION6B277 - 395
7X-RAY DIFFRACTION7B396 - 455
8X-RAY DIFFRACTION8B456 - 741

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