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- PDB-2xzk: THE ASPERGILLUS FUMIGATUS SIALIDASE IS A KDNASE: STRUCTURAL AND M... -

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Basic information

Entry
Database: PDB / ID: 2xzk
TitleTHE ASPERGILLUS FUMIGATUS SIALIDASE IS A KDNASE: STRUCTURAL AND MECHANISTIC INSIGHTS
ComponentsEXTRACELLULAR SIALIDASE/NEURAMINIDASE, PUTATIVE
KeywordsHYDROLASE
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
Chem-FKD / Chem-K99 / NITRATE ION / Exo-alpha-sialidase
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTelford, J.C. / Yeung, J.H.F. / Kiefel, M.J. / Watts, A.G. / Hader, S. / Chan, J. / Bennet, A.J. / Moore, M.M. / Taylor, G.L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Aspergillus Fumigatus Sialidase is a Kdnase: Structural and Mechanistic Insights.
Authors: Telford, J.C. / Yeung, J.H.F. / Xu, G. / Kiefel, M.J. / Watts, A.G. / Hader, S. / Chan, J. / Bennet, A.J. / Moore, M.M. / Taylor, G.L.
History
DepositionNov 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references / Non-polymer description / Version format compliance
Revision 1.2May 16, 2012Group: Other
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 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
A: EXTRACELLULAR SIALIDASE/NEURAMINIDASE, PUTATIVE
B: EXTRACELLULAR SIALIDASE/NEURAMINIDASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,88819
Polymers84,2352
Non-polymers2,65317
Water19,7261095
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A: EXTRACELLULAR SIALIDASE/NEURAMINIDASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1938
Polymers42,1181
Non-polymers1,0757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EXTRACELLULAR SIALIDASE/NEURAMINIDASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,69511
Polymers42,1181
Non-polymers1,57810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.680, 58.080, 94.450
Angle α, β, γ (deg.)90.00, 100.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein EXTRACELLULAR SIALIDASE/NEURAMINIDASE, PUTATIVE / KDNASE


Mass: 42117.703 Da / Num. of mol.: 2 / Fragment: MATURE PROTEIN, RESIDUES 21-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Strain: AF293 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q4WQS0, exo-alpha-sialidase

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Sugars , 2 types, 7 molecules

#2: Sugar ChemComp-FKD / 3-deoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 3-deoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulosonic acid / 3-deoxy-3-fluoro-D-erythro-L-manno-non-2-ulosonic acid / 3-deoxy-3-fluoro-D-erythro-manno-non-2-ulosonic acid


Type: L-saccharide, alpha linking / Mass: 286.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15FO9
#3: Sugar
ChemComp-K99 / (2R,3R,4R,5R,6S)-2,3-bis(fluoranyl)-4,5-bis(oxidanyl)-6-[(1R,2R)-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid / (2R,3R,4R,5R,6S)-2,3-DIFLUORO-4,5-DIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]OXANE-2-CARBOXYLIC ACID


Type: D-saccharide / Mass: 288.199 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H14F2O8

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Non-polymers , 5 types, 1105 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1095 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsCRYSTALLIZED PROTEIN LACKS FIRST 20 AMINO ACIDS (SIGNAL SEQUENCE).

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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: 2.43 Å3/Da / Density % sol: 49.31 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.5→31.1 Å / Num. obs: 129281 / % possible obs: 86.2 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.9
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.5 / % possible all: 47

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XCY

2xcy


Resolution: 1.5→31.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.447 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21375 5515 5 %RANDOM
Rwork0.17923 ---
obs0.18096 105520 85.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.918 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.17 Å2
2--0.1 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5918 0 169 1095 7182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226323
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.978619
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4223.014292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87215965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0191560
X-RAY DIFFRACTIONr_chiral_restr0.0770.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214904
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5491.53854
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94626185
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47932469
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3224.52418
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 177 -
Rwork0.26 3884 -
obs--42.51 %

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