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- PDB-7p1f: Structure of KDNase from Aspergillus terrerus in complex with 2,3... -

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Basic information

Entry
Database: PDB / ID: 7p1f
TitleStructure of KDNase from Aspergillus terrerus in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.
ComponentsSialidase domain-containing protein
KeywordsCARBOHYDRATE / Carbohydrate Metabolism / Enzyme Structure / Protein Structure / KDN / KDNase / Sialic Acid / Sialidase
Function / homology
Function and homology information


exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / intracellular membrane-bounded organelle / membrane / metal ion binding / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
Chem-KFN / Sialidase domain-containing protein
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsGloster, T.M. / McMahon, S.A.
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Kinetic and Structural Characterization of Sialidases (Kdnases) from Ascomycete Fungal Pathogens.
Authors: Nejatie, A. / Steves, E. / Gauthier, N. / Baker, J. / Nesbitt, J. / McMahon, S.A. / Oehler, V. / Thornton, N.J. / Noyovitz, B. / Khazaei, K. / Byers, B.W. / Zandberg, W.F. / Gloster, T.M. / ...Authors: Nejatie, A. / Steves, E. / Gauthier, N. / Baker, J. / Nesbitt, J. / McMahon, S.A. / Oehler, V. / Thornton, N.J. / Noyovitz, B. / Khazaei, K. / Byers, B.W. / Zandberg, W.F. / Gloster, T.M. / Moore, M.M. / Bennet, A.J.
History
DepositionJul 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Sialidase domain-containing protein
A: Sialidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,15310
Polymers89,2042
Non-polymers9498
Water15,709872
1
B: Sialidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0775
Polymers44,6021
Non-polymers4744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sialidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0775
Polymers44,6021
Non-polymers4744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.318, 66.833, 92.813
Angle α, β, γ (deg.)90.000, 90.760, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11B-647-

HOH

21A-677-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B27 - 133
2010A27 - 133
1020B136 - 410
2020A136 - 410

NCS ensembles :
ID
1
2

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Components

#1: Protein Sialidase domain-containing protein


Mass: 44602.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (strain NIH 2624 / FGSC A1156) (mold)
Strain: NIH 2624 / FGSC A1156 / Gene: ATEG_04964 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0CMX0
#2: Sugar ChemComp-KFN / 2,6-anhydro-3-deoxy-D-glycero-D-galacto-non-2-enonic acid / (4S,5R,6R)-4,5-DIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]-5,6-DIHYDRO-4H-PYRAN-2-CARBOXYLIC ACID


Type: D-saccharide / Mass: 250.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C9H14O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 872 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 6K, 0.1M MES pH6 , 0.2M Calcium Chloride

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.29→92.8 Å / Num. obs: 129965 / % possible obs: 96.3 % / Redundancy: 2.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.059 / Net I/σ(I): 7.6
Reflection shellResolution: 1.29→1.31 Å / Rmerge(I) obs: 0.68 / Num. unique obs: 8132 / CC1/2: 0.479 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xzk

2xzk


Resolution: 1.45→92.8 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.148 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 6481 5 %RANDOM
Rwork0.1521 ---
obs0.1544 123439 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 723.02 Å2 / Biso mean: 17.116 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.57 Å2
2---1.08 Å20 Å2
3---0.88 Å2
Refinement stepCycle: final / Resolution: 1.45→92.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5906 0 66 874 6846
Biso mean--20.27 30.11 -
Num. residues----769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.026163
X-RAY DIFFRACTIONr_bond_other_d0.0010.025448
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.958362
X-RAY DIFFRACTIONr_angle_other_deg0.7353.00112630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1422.862283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.30115935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4951558
X-RAY DIFFRACTIONr_chiral_restr0.0790.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217017
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021369
X-RAY DIFFRACTIONr_rigid_bond_restr4.943311609
X-RAY DIFFRACTIONr_sphericity_free28.6795620
X-RAY DIFFRACTIONr_sphericity_bonded14.726511720
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B33860.06
12A33860.06
21B89560.05
22A89560.05
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 404 -
Rwork0.244 9024 -
all-9428 -
obs--96.68 %

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