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- PDB-2ya7: Crystal structure of Streptococcus pneumoniae NanA (TIGR4) in com... -

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Basic information

Entry
Database: PDB / ID: 2ya7
TitleCrystal structure of Streptococcus pneumoniae NanA (TIGR4) in complex with Zanamivir
ComponentsNEURAMINIDASE A
KeywordsHYDROLASE / SIALIDASE
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm
Similarity search - Function
: / 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 / Laminin G domain / Laminin G domain / Sialidase family ...: / 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 / Laminin G domain / Laminin G domain / Sialidase family / Sialidase / YSIRK type signal peptide / Neuraminidase - #10 / YSIRK Gram-positive signal peptide / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Sialidase superfamily / 6 Propeller / Neuraminidase / Concanavalin A-like lectin/glucanase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ZANAMIVIR / : / Sialidase A
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 2, 2020Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _chem_comp.pdbx_synonyms
Revision 1.5May 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
C: NEURAMINIDASE A
D: NEURAMINIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,85812
Polymers221,3874
Non-polymers1,4718
Water23,3111294
1
A: NEURAMINIDASE A
B: NEURAMINIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4296
Polymers110,6932
Non-polymers7364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: NEURAMINIDASE A
D: NEURAMINIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4296
Polymers110,6932
Non-polymers7364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.856, 87.161, 126.410
Angle α, β, γ (deg.)104.06, 91.04, 106.68
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.2855, -0.4617, -0.839), (-0.4649, -0.833, 0.2999), (-0.838, 0.3049, -0.4525)9.979, -95.8, 68.28
2given(1, -0.001879, -0.009256), (-0.00187, -1, 0.000997), (-0.009258, -0.00098, -1)25.28, -115.2, 120.9
3given(0.2889, 0.4637, 0.8376), (-0.4689, 0.8313, -0.2985), (-0.8347, -0.3065, 0.4576)-31.1, 24.63, -42.81

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Components

#1: Protein
NEURAMINIDASE A / NANA


Mass: 55346.684 Da / Num. of mol.: 4 / 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: Sugar
ChemComp-ZMR / ZANAMIVIR / 4-GUANIDINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / 4-guanidino-Neu5Ac2en / MODIFIED SIALIC ACID


Type: D-saccharide / Mass: 332.310 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H20N4O7 / Comment: medication*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1294 / 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: 2.3 Å3/Da / Density % sol: 46.5 % / 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: 1.9→30 Å / Num. obs: 148783 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.5 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→27.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.027 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25692 3718 2.5 %RANDOM
Rwork0.20759 ---
obs0.20881 145055 100 %-
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: 32.432 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.89→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14856 0 96 1294 16246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02215425
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.95220870
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47251907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78924.458747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88152693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5681599
X-RAY DIFFRACTIONr_chiral_restr0.0820.22198
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211887
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.27413
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.210426
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.21578
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6881.59642
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.171215127
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.50836653
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3194.55743
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: 1.892→1.941 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 233 -
Rwork0.266 9712 -
obs--100 %

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