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- PDB-4yz1: Crystal Structure of Streptococcus pneumoniae NanC, apo structure. -

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Basic information

Entry
Database: PDB / ID: 4yz1
TitleCrystal Structure of Streptococcus pneumoniae NanC, apo structure.
ComponentsPutative neuraminidase
KeywordsTRANSFERASE / Sialidase / Neuraminidase / Beta-propeller / propeller / CBM40
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 / 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 / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / 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 / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / 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
Putative neuraminidase / Putative neuraminidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsLukacik, P. / Owen, D.O. / 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 2.0Sep 13, 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 2.1Jan 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: Putative neuraminidase
B: Putative neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,14614
Polymers151,9942
Non-polymers1,15312
Water14,736818
1
A: Putative neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5737
Polymers75,9971
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5737
Polymers75,9971
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.134, 73.736, 136.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 84 - 740 / Label seq-ID: 21 - 677

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

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Components

#1: Protein Putative neuraminidase /


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 serotype 4 (bacteria)
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 818 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.76 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.25M Ammonium sulfate, 0.1M pH8, 7.5% Ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9253 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9253 Å / Relative weight: 1
ReflectionResolution: 1.969→136.1 Å / Num. obs: 107569 / % possible obs: 98.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.9
Reflection shellResolution: 1.97→1.99 Å / Redundancy: 3 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.93 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JKB

2jkb


Resolution: 1.97→101.05 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.368 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21519 5286 5 %RANDOM
Rwork0.18125 ---
obs0.18295 100672 98.52 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.29 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å2-0 Å2
2---1.56 Å20 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.97→101.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10396 0 60 818 11274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0210725
X-RAY DIFFRACTIONr_bond_other_d0.0040.029941
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9514554
X-RAY DIFFRACTIONr_angle_other_deg1.091322910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38451320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18324.741502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.258151810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8691546
X-RAY DIFFRACTIONr_chiral_restr0.10.21584
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212251
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022519
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_it1.8311.6525265
X-RAY DIFFRACTIONr_mcbond_other1.8311.6525264
X-RAY DIFFRACTIONr_mcangle_it2.5572.4666581
X-RAY DIFFRACTIONr_mcangle_other2.5572.4666582
X-RAY DIFFRACTIONr_scbond_it3.0661.9875460
X-RAY DIFFRACTIONr_scbond_other2.9251.9525412
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.42.7867898
X-RAY DIFFRACTIONr_long_range_B_refined6.54314.25112482
X-RAY DIFFRACTIONr_long_range_B_other6.48313.82612175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 83744 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.969→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 400 -
Rwork0.29 7313 -
obs--98.14 %
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)
10.8496-0.1486-0.04561.10280.01070.3614-0.0223-0.0937-0.03420.04460.01090.0350.0008-0.01530.01150.0149-0.0057-0.01990.01820.00670.0976144.02937.64634.487
20.81150.2136-0.00060.9153-0.00980.3666-0.04010.086-0.0386-0.05550.0279-0.02030.0090.01690.01230.0140.0043-0.01630.0194-0.00920.1036156.21823.617-34.416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A84 - 740
2X-RAY DIFFRACTION2B83 - 740

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