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- PDB-7mhu: Sialidase24 apo -

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Basic information

Entry
Database: PDB / ID: 7mhu
TitleSialidase24 apo
ComponentsExo-alpha-sialidase
KeywordsHYDROLASE / Sialidase / microbiome / sialic acid / inflammation
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
BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacteroides acidifaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRees, S.D. / Chang, G.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-1444435 United States
CitationJournal: Proteins / Year: 2021
Title: Computational models in the service of X-ray and cryo-electron microscopy structure determination.
Authors: Kryshtafovych, A. / Moult, J. / Albrecht, R. / Chang, G.A. / Chao, K. / Fraser, A. / Greenfield, J. / Hartmann, M.D. / Herzberg, O. / Josts, I. / Leiman, P.G. / Linden, S.B. / Lupas, A.N. / ...Authors: Kryshtafovych, A. / Moult, J. / Albrecht, R. / Chang, G.A. / Chao, K. / Fraser, A. / Greenfield, J. / Hartmann, M.D. / Herzberg, O. / Josts, I. / Leiman, P.G. / Linden, S.B. / Lupas, A.N. / Nelson, D.C. / Rees, S.D. / Shang, X. / Sokolova, M.L. / Tidow, H.
History
DepositionApr 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exo-alpha-sialidase
B: Exo-alpha-sialidase


Theoretical massNumber of molelcules
Total (without water)91,5542
Polymers91,5542
Non-polymers00
Water1,40578
1
A: Exo-alpha-sialidase


Theoretical massNumber of molelcules
Total (without water)45,7771
Polymers45,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exo-alpha-sialidase


Theoretical massNumber of molelcules
Total (without water)45,7771
Polymers45,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.109, 141.109, 54.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Exo-alpha-sialidase / Sialidase24


Mass: 45777.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides acidifaciens (bacteria) / Gene: E5356_01515 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A4S2B3K9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-Tris, 20% polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→29.62 Å / Num. obs: 73015 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.272 / Net I/σ(I): 6.4
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 4481 / CC1/2: 0.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
MOSFLM7.3.0data reduction
Aimless0.7.4data scaling
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold T1089TS427_2

Resolution: 2→29.62 Å / Cross valid method: FREE R-VALUE / σ(F): 143.18 / Phase error: 40.02 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2054 3517 4.82 %
Rwork0.1888 --
obs0.196 72960 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5756 0 0 78 5834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055894
X-RAY DIFFRACTIONf_angle_d0.7347998
X-RAY DIFFRACTIONf_dihedral_angle_d5.77802
X-RAY DIFFRACTIONf_chiral_restr0.048866
X-RAY DIFFRACTIONf_plane_restr0.0051028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.33551860.33163429X-RAY DIFFRACTION94
2.03-2.070.30771500.31933450X-RAY DIFFRACTION96
2.07-2.110.31191540.31893472X-RAY DIFFRACTION96
2.11-2.150.28681780.31293434X-RAY DIFFRACTION95
2.15-2.20.32221750.30583448X-RAY DIFFRACTION95
2.2-2.250.33581580.31443472X-RAY DIFFRACTION96
2.25-2.310.31941260.30633461X-RAY DIFFRACTION96
2.31-2.370.32091730.30413505X-RAY DIFFRACTION95
2.37-2.440.35381830.28943422X-RAY DIFFRACTION95
2.44-2.520.3022020.2773453X-RAY DIFFRACTION94
2.52-2.610.30521700.26483479X-RAY DIFFRACTION95
2.61-2.710.26131700.25623465X-RAY DIFFRACTION95
2.71-2.840.26081820.23633440X-RAY DIFFRACTION95
2.84-2.990.24311740.22193475X-RAY DIFFRACTION95
2.99-3.170.23271810.20173464X-RAY DIFFRACTION95
3.17-3.420.22671930.17973482X-RAY DIFFRACTION95
3.42-3.760.1851700.16223478X-RAY DIFFRACTION95
3.76-4.30.16751850.13163489X-RAY DIFFRACTION95
4.31-5.420.14032030.1173532X-RAY DIFFRACTION95
5.42-29.620.16662040.15083593X-RAY DIFFRACTION95

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