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- PDB-2ya4: Crystal structure of Streptococcus pneumoniae NanA (TIGR4) -

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Basic information

Entry
Database: PDB / ID: 2ya4
TitleCrystal structure of Streptococcus pneumoniae NanA (TIGR4)
ComponentsNEURAMINIDASE A
KeywordsHYDROLASE / SIALIDASE
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm
Similarity search - Function
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 / Laminin G domain / Laminin G domain / Sialidase family / Sialidase ...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 / Laminin G domain / Laminin G domain / Sialidase family / Sialidase / YSIRK type signal peptide / Neuraminidase - #10 / YSIRK Gram-positive signal peptide / Sialidase superfamily / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / 6 Propeller / Neuraminidase / Concanavalin A-like lectin/glucanase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / : / Sialidase A
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGut, H. / Xu, G. / Taylor, G.L. / Walsh, M.A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Basis for Streptococcus Pneumoniae Nana Inhibition by Influenza Antivirals Zanamivir and Oseltamivir Carboxylate.
Authors: Gut, H. / Xu, G. / Taylor, G.L. / Walsh, M.A.
History
DepositionFeb 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 2, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_site
Item: _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id ..._pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURAMINIDASE A
B: NEURAMINIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,59720
Polymers110,6932
Non-polymers90418
Water15,097838
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint5 kcal/mol
Surface area35010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.420, 48.864, 125.247
Angle α, β, γ (deg.)90.00, 104.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8313, -0.4703, 0.2961), (-0.4772, 0.331, -0.8141), (0.2849, -0.8181, -0.4996)
Vector: 95.82, -7.541, -68.04)

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Components

#1: Protein NEURAMINIDASE A / NANA


Mass: 55346.684 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 280-754
Source method: isolated from a genetically manipulated source
Details: THE SEQUENCE NUMBERING ABOVE CORRESPONDS TO THE CLOSEST UNIPROT SEQUENCE MATCH UNP B2DJD9. THE SEQUENCE NUMBERING FOR THE ENTRY SHOULD BE 303-777
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: B2DJD9, UniProt: P62575*PLUS, exo-alpha-sialidase
#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 838 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHYPOTHETICAL PROTEIN SPNET_02001817 STREPTOCOCCUS PNEUMONIAE TIGR4. APPARENT CONFLICTS ARE DUE TO ...HYPOTHETICAL PROTEIN SPNET_02001817 STREPTOCOCCUS PNEUMONIAE TIGR4. APPARENT CONFLICTS ARE DUE TO CURRENT UNIPROT MAPPING. SEQUENCE REFERENCE: UNIREF100_UPI00005582E2.

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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: 2.22 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growDetails: 20% PEG 3350, 200 MM KFORMATE, 20 MM TRIS PH 7.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2007 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI 111 CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 88780 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.6 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→24.86 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.163 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23411 2233 2.5 %RANDOM
Rwork0.19099 ---
obs0.19209 86544 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.208 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7449 0 56 838 8343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227761
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9510472
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0415963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3724.507375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.098151366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0721549
X-RAY DIFFRACTIONr_chiral_restr0.090.21095
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025961
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.23771
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25221
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2882
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7511.54871
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2627625
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67233317
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5824.52847
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 127 -
Rwork0.266 5308 -
obs--82.86 %

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