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- PDB-6tvi: Salmonella typhimurium mutant neuraminidase (D100S)+ DANA -

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Basic information

Entry
Database: PDB / ID: 6tvi
TitleSalmonella typhimurium mutant neuraminidase (D100S)+ DANA
ComponentsSialidase
KeywordsHYDROLASE / Salmonella Typhimurium enzyme / complex / DANA / D100S mutant neuraminidase complexed with DANA / sialidase
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Sialidase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsGarman, E.F. / Salinger, M.T. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Vimr, E.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Salmonella typhimurium mutant neuraminidase (D100S)+ DANA
Authors: Garman, E.F. / Salinger, M.T. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Vimr, E.R.
History
DepositionJan 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Category: chem_comp / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6078
Polymers41,7641
Non-polymers8447
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint0 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.068, 81.781, 91.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sialidase / N-acylneuraminate glycohydrolase / Neuraminidase / NANase / STNA


Mass: 41763.547 Da / Num. of mol.: 1 / Mutation: D100S
Source method: isolated from a genetically manipulated source
Details: DANA: 2-deoxy-2,3-dehydro-n-acetyl-neuraminic acid
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: nanH, STM0928 / Plasmid: pSELECT-nanH / Cell line (production host): JM109 / Production host: Escherichia coli (E. coli) / References: UniProt: P29768, exo-alpha-sialidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of 15mg/ml protein solution and an 8:4 mixture of 3.0M K2HPO4 to 1.4M KH2P04 was placed above a well of an 8:6 solution of 3.0M ...Details: Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of 15mg/ml protein solution and an 8:4 mixture of 3.0M K2HPO4 to 1.4M KH2P04 was placed above a well of an 8:6 solution of 3.0M K2HPO4 to 1.4M KH2PO4. Then serially cryoprotected in situ to 40% glycerol (v/v with mother liquor) in 10% increments over a period of a few minutes.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→21.96 Å / Num. obs: 188880 / % possible obs: 99.7 % / Redundancy: 5 % / Biso Wilson estimate: 6.4 Å2 / Rrim(I) all: 0.091 / Net I/σ(I): 11.5
Reflection shellResolution: 1→1.02 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 9266 / Rrim(I) all: 0.573 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SIL

3sil


Resolution: 1→21.959 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.129 / WRfactor Rwork: 0.115 / SU B: 0.429 / SU ML: 0.01 / Average fsc free: 0.9796 / Average fsc work: 0.982 / Cross valid method: FREE R-VALUE / ESU R: 0.019 / ESU R Free: 0.02
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1332 5722 3.029 %
Rwork0.1184 183158 -
all0.119 --
obs-188880 99.588 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 8.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.026 Å2-0 Å2-0 Å2
2---0.071 Å20 Å2
3---0.044 Å2
Refinement stepCycle: LAST / Resolution: 1→21.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 56 487 3481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0133416
X-RAY DIFFRACTIONr_bond_other_d0.0030.0183124
X-RAY DIFFRACTIONr_angle_refined_deg2.281.6454654
X-RAY DIFFRACTIONr_angle_other_deg1.6451.5897315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.0685.195461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85122.767159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1615603
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg2.581152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5121517
X-RAY DIFFRACTIONr_chiral_restr0.1360.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024172
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02715
X-RAY DIFFRACTIONr_nbd_refined0.2870.2683
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.23085
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21611
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.21700
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2384
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.30.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.230
X-RAY DIFFRACTIONr_nbd_other0.230.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.251
X-RAY DIFFRACTIONr_mcbond_it1.460.6551712
X-RAY DIFFRACTIONr_mcbond_other1.4590.6541711
X-RAY DIFFRACTIONr_mcangle_it1.6530.9922200
X-RAY DIFFRACTIONr_mcangle_other1.6540.9922201
X-RAY DIFFRACTIONr_scbond_it2.2130.9051704
X-RAY DIFFRACTIONr_scbond_other2.2120.9051705
X-RAY DIFFRACTIONr_scangle_it2.971.2612453
X-RAY DIFFRACTIONr_scangle_other2.971.262454
X-RAY DIFFRACTIONr_lrange_it3.23910.0984027
X-RAY DIFFRACTIONr_lrange_other3.23810.0974028
X-RAY DIFFRACTIONr_rigid_bond_restr8.23936540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.0260.2133920.19813483X-RAY DIFFRACTION99.9208
1.026-1.0540.1784150.16713058X-RAY DIFFRACTION99.8
1.054-1.0850.1524100.13812782X-RAY DIFFRACTION99.758
1.085-1.1180.1063640.112406X-RAY DIFFRACTION99.7968
1.118-1.1550.1023820.07911994X-RAY DIFFRACTION99.5896
1.155-1.1950.0973640.07711526X-RAY DIFFRACTION99.2405
1.195-1.240.0943830.07511248X-RAY DIFFRACTION99.7513
1.24-1.2910.0943570.07710786X-RAY DIFFRACTION100
1.291-1.3480.0983210.08410458X-RAY DIFFRACTION100
1.348-1.4140.0963330.0929927X-RAY DIFFRACTION100
1.414-1.4910.1172950.0999483X-RAY DIFFRACTION99.8672
1.491-1.5810.12940.098949X-RAY DIFFRACTION99.5584
1.581-1.690.1152650.0878439X-RAY DIFFRACTION99.8051
1.69-1.8250.12420.0897903X-RAY DIFFRACTION99.8039
1.825-20.1142310.1087262X-RAY DIFFRACTION99.8667
2-2.2350.1411900.126657X-RAY DIFFRACTION100
2.235-2.5810.191680.1615873X-RAY DIFFRACTION99.8347
2.581-3.1610.1891350.1764997X-RAY DIFFRACTION99.1499
3.161-4.4670.1681200.1443797X-RAY DIFFRACTION97.0275
4.467-21.9590.218610.1882130X-RAY DIFFRACTION92.7997

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