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- PDB-1sli: LEECH INTRAMOLECULAR TRANS-SIALIDASE COMPLEXED WITH DANA -

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Basic information

Entry
Database: PDB / ID: 1sli
TitleLEECH INTRAMOLECULAR TRANS-SIALIDASE COMPLEXED WITH DANA
ComponentsINTRAMOLECULAR TRANS-SIALIDASE
KeywordsHYDROLASE / INTRAMOLECULAR TRANS-SIALIDASE / NEURAMINIDASE
Function / homology
Function and homology information


anhydrosialidase / anhydrosialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm
Similarity search - Function
Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily ...Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / 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
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Anhydrosialidase
Similarity search - Component
Biological speciesMacrobdella decora (North American leech)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2 Å
AuthorsLuo, Y. / Li, S.C. / Chou, M.Y. / Li, Y.T. / Luo, M.
CitationJournal: Structure / Year: 1998
Title: The crystal structure of an intramolecular trans-sialidase with a NeuAc alpha2-->3Gal specificity.
Authors: Luo, Y. / Li, S.C. / Chou, M.Y. / Li, Y.T. / Luo, M.
History
DepositionMar 28, 1998Processing site: BNL
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_database_status.process_site / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTRAMOLECULAR TRANS-SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8572
Polymers74,5661
Non-polymers2911
Water11,115617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.443, 69.516, 72.514
Angle α, β, γ (deg.)113.14, 95.39, 106.87
Int Tables number1
Space group name H-MP1

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Components

#1: Protein INTRAMOLECULAR TRANS-SIALIDASE


Mass: 74565.688 Da / Num. of mol.: 1 / Fragment: DEVOID OF N-TERMINAL 28 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macrobdella decora (North American leech)
Gene: T7 / Plasmid: E2-M10 / Species (production host): Escherichia coli / Gene (production host): T7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q27701, exo-alpha-sialidase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.4 Å3/Da / Density % sol: 40 %
Crystal growpH: 6.3 / Details: pH 6.3
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlenzyme1drop
20.1 Mcacodylate1reservoir
320 %PEG60001reservoir
40.25 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 24, 1997 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 53170 / % possible obs: 74 % / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 9.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.248 / % possible all: 56.3
Reflection
*PLUS
Num. measured all: 72285
Reflection shell
*PLUS
% possible obs: 56.3 %

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Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.85phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: NATIVE STRUCTURE

Resolution: 2→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.224 -10 %RANDOM
Rwork0.167 ---
obs0.167 47213 93.4 %-
Displacement parametersBiso mean: 11.9 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5257 0 0 681 5938
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
X-RAY DIFFRACTION3PARAM3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 52955 / Rfactor obs: 0.182 / Rfactor Rfree: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.61
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_deg1.28

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