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- PDB-4yz2: Crystal Structure of Streptococcus pneumoniae NanC, in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4yz2
TitleCrystal Structure of Streptococcus pneumoniae NanC, in complex with 2-deoxy-2,3-didehydro-N-acetylneuraminic acid.
ComponentsSialidase NanC
KeywordsHYDROLASE / Sialidase / Neuraminidase / Beta-propeller / CBM40
Function / homology
Function and homology information


: / : / : / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / 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
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / exo-alpha-sialidase / Putative neuraminidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsLukacik, P. / Owen, C.D. / Potter, J.A. / Taylor, G.L. / Walsh, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) 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 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Sialidase NanC
B: Sialidase NanC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,53714
Polymers151,9942
Non-polymers1,54312
Water16,340907
1
A: Sialidase NanC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7687
Polymers75,9971
Non-polymers7726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sialidase NanC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7687
Polymers75,9971
Non-polymers7726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.300, 136.710, 150.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 84 - 739 / Label seq-ID: 21 - 676

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

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Components

#1: Protein Sialidase NanC


Mass: 75996.844 Da / Num. of mol.: 2 / Fragment: UNP residues 84-740
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1326 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS
References: UniProt: Q97Q99, UniProt: A0A0H2UQE4*PLUS, exo-alpha-sialidase
#2: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO8
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 907 / 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: 2.49 Å3/Da / Density % sol: 50.51 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.25M Ammonium sulfate, 0.1M Hepes pH8, 7.5% Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.06→101.28 Å / Num. obs: 93784 / % possible obs: 99.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.1
Reflection shellResolution: 2.06→2.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
xia20.3.3.1data reduction
xia20.3.3.1data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→101.28 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.643 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 4695 5 %RANDOM
Rwork0.2065 ---
obs0.2084 89017 99.34 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 115.5 Å2 / Biso mean: 15.88 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0 Å20 Å2
2--1.11 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 2.06→101.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10388 0 90 907 11385
Biso mean--39.64 19.82 -
Num. residues----1311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0210749
X-RAY DIFFRACTIONr_bond_other_d0.0050.029959
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.95314587
X-RAY DIFFRACTIONr_angle_other_deg1.147322957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46651319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2224.731501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.192151809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1011546
X-RAY DIFFRACTIONr_chiral_restr0.1060.21591
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212274
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022524
X-RAY DIFFRACTIONr_mcbond_it1.4770.7045261
X-RAY DIFFRACTIONr_mcbond_other1.4760.7045260
X-RAY DIFFRACTIONr_mcangle_it2.0931.0476576
Refine LS restraints NCS

Ens-ID: 1 / Number: 83084 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.06→2.114 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 324 -
Rwork0.287 6527 -
all-6851 -
obs--99.33 %
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)
10.4581-0.0135-0.03090.20310.07180.5826-0.00260.00960.00020.00670.0118-0.0159-0.04980.0273-0.00910.016-0.0052-0.00810.01270.01440.0486-0.5634.4516.271
20.4261-0.01660.01810.23470.07170.53310.0028-0.0126-0.0064-0.0156-0.0076-0.01070.0291-0.00210.00480.0119-0.00020.00970.01110.01480.047213.552-34.443-6.243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A84 - 740
2X-RAY DIFFRACTION2B83 - 740

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