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- PDB-7af2: Salmonella typhimurium neuraminidase mutant (D62G) -

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Basic information

Entry
Database: PDB / ID: 7af2
TitleSalmonella typhimurium neuraminidase mutant (D62G)
ComponentsSialidase
KeywordsHYDROLASE / Salmonella typhimurium / enzyme / neuraminidase / mutant / D62G / sialidase / native / hydrolase.
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
PHOSPHATE ION / Sialidase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.792 Å
AuthorsSalinger, M.T. / Kuhn, P. / Laver, W.G. / Pape, T. / Schneider, T.R. / Sheldrick, G.M. / Vimr, E.R. / Garman, E.F.
CitationJournal: To Be Published
Title: Salmonella typhimurium neuraminidase mutant (D62G)
Authors: Garman, E.F. / Salinger, M.T. / Laver, W.G. / Kuhn, P. / Pape, T. / Schneider, T.R. / Sheldrick, G.M. / Vimr, E.R.
History
DepositionSep 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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)42,2897
Polymers41,7341
Non-polymers5556
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-4 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.914, 81.357, 91.053
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: 41733.520 Da / Num. of mol.: 1 / Mutation: D62G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: nanH, STM0928 / 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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of protein solution and an 8:4 mixture of K2HPO4 to KH2PO4 was placed above a well of an 8:6 solution of K2HPO4 to KH2PO4. Then ...Details: Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of protein solution and an 8:4 mixture of K2HPO4 to KH2PO4 was placed above a well of an 8:6 solution of K2HPO4 to 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: BL9-1 / Wavelength: 0.79 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 27, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79 Å / Relative weight: 1
ReflectionResolution: 0.792→18.107 Å / Num. obs: 355798 / % possible obs: 94.7 % / Redundancy: 3.2 % / Rrim(I) all: 0.061 / Rsym value: 0.053 / Net I/σ(I): 23.61
Reflection shellResolution: 0.792→0.81 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.88 / Num. unique obs: 19346 / Rrim(I) all: 1.572 / Rsym value: 1.161 / % possible all: 70.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SIL

3sil


Resolution: 0.792→18.102 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.986 / WRfactor Rfree: 0.14 / WRfactor Rwork: 0.126 / Average fsc free: 0.8265 / Average fsc work: 0.829 / Cross valid method: FREE R-VALUE / ESU R: 0.011 / ESU R Free: 0.012
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1319 17531 5.018 %
Rwork0.1206 331837 -
all0.121 --
obs-349368 92.919 %
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: 15.115 Å2
Baniso -1Baniso -2Baniso -3
1-0.408 Å20 Å2-0 Å2
2---0.283 Å20 Å2
3----0.125 Å2
Refinement stepCycle: LAST / Resolution: 0.792→18.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2936 0 35 502 3473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0133366
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173091
X-RAY DIFFRACTIONr_angle_refined_deg2.4681.6494580
X-RAY DIFFRACTIONr_angle_other_deg2.521.597240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9315428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89223.333168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7715611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5031517
X-RAY DIFFRACTIONr_chiral_restr0.1440.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023820
X-RAY DIFFRACTIONr_gen_planes_other0.020.02691
X-RAY DIFFRACTIONr_nbd_refined0.2910.2651
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2320.22984
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21554
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21547
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2391
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.215
X-RAY DIFFRACTIONr_nbd_other0.1890.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2590.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.210.21
X-RAY DIFFRACTIONr_mcbond_it4.9091.3521652
X-RAY DIFFRACTIONr_mcbond_other4.9111.3511650
X-RAY DIFFRACTIONr_mcangle_it5.8831.9992100
X-RAY DIFFRACTIONr_mcangle_other5.8821.9992101
X-RAY DIFFRACTIONr_scbond_it7.0051.5691714
X-RAY DIFFRACTIONr_scbond_other7.0031.5691715
X-RAY DIFFRACTIONr_scangle_it5.9942.2542480
X-RAY DIFFRACTIONr_scangle_other5.9932.2542481
X-RAY DIFFRACTIONr_lrange_it6.7617.7153932
X-RAY DIFFRACTIONr_lrange_other6.78216.8653774
X-RAY DIFFRACTIONr_rigid_bond_restr15.1136451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.792-0.8131.9437552.09914472X-RAY DIFFRACTION55.0984
0.813-0.8350.76310900.72320624X-RAY DIFFRACTION80.7122
0.835-0.8590.46312730.47323377X-RAY DIFFRACTION94.1127
0.859-0.8850.35212250.35823428X-RAY DIFFRACTION96.8113
0.885-0.9140.28712010.27822701X-RAY DIFFRACTION96.9183
0.914-0.9470.22711010.2322062X-RAY DIFFRACTION97.1725
0.947-0.9820.19811550.18521270X-RAY DIFFRACTION97.3138
0.982-1.0220.16111030.14720572X-RAY DIFFRACTION97.407
1.022-1.0680.14110200.11719708X-RAY DIFFRACTION97.3465
1.068-1.120.11410190.09718718X-RAY DIFFRACTION96.8592
1.12-1.1810.1099540.09117811X-RAY DIFFRACTION96.6371
1.181-1.2520.1058960.0916741X-RAY DIFFRACTION95.8793
1.252-1.3390.1148150.09115942X-RAY DIFFRACTION96.7941
1.339-1.4460.18070.08415333X-RAY DIFFRACTION99.9876
1.446-1.5840.1017440.08514110X-RAY DIFFRACTION100
1.584-1.7710.116830.09112852X-RAY DIFFRACTION100
1.771-2.0440.1156240.111347X-RAY DIFFRACTION99.9833
2.044-2.5040.1284930.1159651X-RAY DIFFRACTION99.9507
2.504-3.5390.1423910.137473X-RAY DIFFRACTION98.497
3.539-18.1020.1371820.1513646X-RAY DIFFRACTION83.7453

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