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- PDB-4yw1: Crystal Structure of Streptococcus pneumoniae NanC, complex with ... -

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Basic information

Entry
Database: PDB / ID: 4yw1
TitleCrystal Structure of Streptococcus pneumoniae NanC, complex with Neu5Ac and Neu5Ac2en following soaking with 3'SL
ComponentsNeuraminidase C
KeywordsHYDROLASE / Sialidase / CBM40
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / 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
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / N-acetyl-alpha-neuraminic acid / exo-alpha-sialidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / 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 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Jun 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_fragment ..._chem_comp.pdbx_synonyms / _entity.pdbx_fragment / _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_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 2.3Jan 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)149,2669
Polymers147,9572
Non-polymers1,3097
Water15,439857
1
A: Neuraminidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4894
Polymers73,9791
Non-polymers5103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neuraminidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7775
Polymers73,9791
Non-polymers7994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.834, 74.945, 113.302
Angle α, β, γ (deg.)90.000, 96.350, 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 , 1 types, 2 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

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Sugars , 2 types, 3 molecules

#2: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8

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Non-polymers , 4 types, 861 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / 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 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. obs: 75606 / % possible obs: 94.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.121 / Χ2: 2.369 / Net I/av σ(I): 11.641 / Net I/σ(I): 8.3 / Num. measured all: 197232
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.25-2.292.50.48239001.87397.8
2.29-2.332.50.46438822.00297.7
2.33-2.382.50.44638671.97997.2
2.38-2.422.50.41938482.04396.9
2.42-2.482.50.39238431.99897.2
2.48-2.532.50.39138552.01296.7
2.53-2.62.50.36838332.08896.5
2.6-2.672.50.31938212.195.9
2.67-2.752.50.29438062.11495.7
2.75-2.832.50.27437922.24295.2
2.83-2.942.50.23837752.2894.6
2.94-3.052.50.18737702.45994.3
3.05-3.192.60.14737402.48394.5
3.19-3.362.70.10738082.63894.7
3.36-3.572.70.08537672.94193.9
3.57-3.852.80.07637403.03593.4
3.85-4.232.70.07337062.88992.5
4.23-4.842.70.05936532.80390.6
4.84-6.12.80.06336322.689.9
6.1-402.80.05135682.48485.8

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

2vw2


Resolution: 2.25→40 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2076 / WRfactor Rwork: 0.1756 / FOM work R set: 0.7904 / SU B: 13.023 / SU ML: 0.167 / SU R Cruickshank DPI: 0.3217 / SU Rfree: 0.2315 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 3803 5 %RANDOM
Rwork0.2087 ---
obs0.2107 71657 94.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 140.99 Å2 / Biso mean: 32.918 Å2 / Biso min: 11.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20.72 Å2
2--1.47 Å20 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 2.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10444 0 84 857 11385
Biso mean--32.08 33.82 -
Num. residues----1318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0210764
X-RAY DIFFRACTIONr_bond_other_d0.0040.0210012
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.95314590
X-RAY DIFFRACTIONr_angle_other_deg1.056323080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26851316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09824.741502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.159151814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0111546
X-RAY DIFFRACTIONr_chiral_restr0.0780.21590
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212272
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022522
X-RAY DIFFRACTIONr_mcbond_it1.4951.1315270
X-RAY DIFFRACTIONr_mcbond_other1.4941.1315269
X-RAY DIFFRACTIONr_mcangle_it2.3161.696584
Refine LS restraints NCS

Ens-ID: 1 / Number: 82932 / 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: 2.249→2.307 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 273 -
Rwork0.258 5369 -
all-5642 -
obs--95.58 %
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)
11.609-0.96680.13631.73530.16630.25940.0257-0.0018-0.14680.0190.00190.06410.07580.0245-0.02750.2156-0.0086-0.16950.01380.00950.22236.688-2.99146.899
21.0394-0.280.64141.44860.04222.5912-0.0086-0.02440.00490.03590.03310.1807-0.1389-0.0221-0.02460.1779-0.0063-0.16460.00220.00480.271420.51725.38655
34.7427-1.3730.55871.80290.35752.5451-0.1525-0.43360.24580.09870.05840.1716-0.3604-0.2440.0940.30440.0084-0.11640.1005-0.01880.224414.47537.25474.222
40.7288-0.17830.42720.85750.15621.23070.0230.03770.0027-0.1317-0.040.1519-0.1133-0.16960.01690.20680.0074-0.18740.04150.01850.26887.87123.09243.919
50.99810.5259-0.41061.9317-0.51920.9485-0.01860.0317-0.08190.0121-0.00650.06870.2339-0.11930.0250.346-0.0172-0.13290.0306-0.00650.26311.722-29.1137.542
60.90970.5317-0.02891.33-0.67611.9460.07350.05240.01340.11070.0220.0342-0.0667-0.0078-0.09560.22330.0177-0.15180.00860.01740.273821.7310.828-6.086
72.2791.4857-1.78574.1536-2.54182.61510.07730.13070.19780.08310.04340.1224-0.2731-0.0648-0.12080.26350.0427-0.13350.09430.02750.225621.49316.808-27.215
80.71220.01330.14440.7691-0.45621.58270.039-0.03690.01350.1101-0.0884-0.1232-0.13790.25050.04930.2515-0.024-0.17050.04520.01110.269533.5090.67-0.029
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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