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- PDB-4c1w: Carbohydrate binding domain from Streptococcus pneumoniae NanA si... -

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Basic information

Entry
Database: PDB / ID: 4c1w
TitleCarbohydrate binding domain from Streptococcus pneumoniae NanA sialidase complexed with 3'-sialyllactose
ComponentsNEURAMINIDASE
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE-BINDING MODULE / SIALIC ACID BINDING
Function / homology
Function and homology information


exo-alpha-sialidase activity / exo-alpha-sialidase / carbohydrate metabolic process
Similarity search - Function
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 / Sialidase superfamily / Jelly Rolls - #200 ...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 / Sialidase superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
3'-sialyl-alpha-lactose / exo-alpha-sialidase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.84 Å
AuthorsYang, L. / Connaris, H. / Potter, J.A. / Taylor, G.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Prevention of Influenza by Targeting Host Receptors Using Engineered Proteins.
Authors: Connaris, H. / Govorkova, E.A. / Ligertwood, Y. / Dutia, B.M. / Yang, L. / Tauber, S. / Taylor, M.A. / Alias, N. / Hagan, R. / Nash, A.A. / Webster, R.G. / Taylor, G.L.
History
DepositionAug 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8223
Polymers21,0671
Non-polymers7562
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.567, 44.517, 42.982
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NEURAMINIDASE


Mass: 21066.666 Da / Num. of mol.: 1 / Fragment: CBM40, RESIDUES 52-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R36A / NCTC 10319 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4LB86
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / 3'-sialyl-alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-alpha-lactose
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 1.92 Å3/Da / Density % sol: 36 % / Description: NONE
Crystal growpH: 9 / Details: pH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→44.5 Å / Num. obs: 12277 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 38.7
Reflection shellResolution: 1.84→1.9 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 16.8 / % possible all: 75.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.84→44.52 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.721 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19784 645 5 %RANDOM
Rwork0.14261 ---
obs0.14539 12277 92.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.665 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-1 Å2
2--0.46 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.84→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 51 170 1703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021613
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0391.992196
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4855199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.58824.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33215279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1181511
X-RAY DIFFRACTIONr_chiral_restr0.1780.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211208
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.841→1.889 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 43 -
Rwork0.168 785 -
obs--82.39 %

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