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- PDB-7p1v: Apo structure of KDNase from Trichophyton Rubrum -

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Basic information

Entry
Database: PDB / ID: 7p1v
TitleApo structure of KDNase from Trichophyton Rubrum
ComponentsExtracellular sialidase/neuraminidase
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
Extracellular sialidase/neuraminidase
Similarity search - Component
Biological speciesTrichophyton rubrum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsGloster, T.M. / McMahon, S.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
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 2, 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 1.2Jan 31, 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

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Assembly

Deposited unit
A: Extracellular sialidase/neuraminidase
B: Extracellular sialidase/neuraminidase
C: Extracellular sialidase/neuraminidase
D: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,77513
Polymers178,1554
Non-polymers6219
Water30,4631691
1
A: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6713
Polymers44,5391
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6713
Polymers44,5391
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7634
Polymers44,5391
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6713
Polymers44,5391
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.030, 180.850, 98.340
Angle α, β, γ (deg.)90.000, 103.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A26 - 409
2010B26 - 409
1020A26 - 405
2020C26 - 405
1030A26 - 409
2030D26 - 409
1040B26 - 405
2040C26 - 405
1050B26 - 409
2050D26 - 409
1060C26 - 405
2060D26 - 405

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Extracellular sialidase/neuraminidase


Mass: 44538.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichophyton rubrum (fungus) / Gene: A7C99_5399 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A178EUH2
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1691 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium chloride dihydrate 0.1 M MES 6.0 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9688 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 1.47→47.4 Å / Num. obs: 276720 / % possible obs: 98.5 % / Redundancy: 3.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.3
Reflection shellResolution: 1.47→1.51 Å / Rmerge(I) obs: 0.775 / Num. unique obs: 20438 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xcy

2xcy


Resolution: 1.47→47.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.665 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 13545 4.9 %RANDOM
Rwork0.1744 ---
obs0.1767 263109 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.18 Å2 / Biso mean: 25.74 Å2 / Biso min: 10.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å2-0.09 Å2
2---0.46 Å20 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 1.47→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11773 0 34 1714 13521
Biso mean--28.39 39.47 -
Num. residues----1533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912168
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210904
X-RAY DIFFRACTIONr_angle_refined_deg1.351.94416509
X-RAY DIFFRACTIONr_angle_other_deg0.752325354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47151555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33923.381559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.396151947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.82315109
X-RAY DIFFRACTIONr_chiral_restr0.0810.21736
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022555
X-RAY DIFFRACTIONr_rigid_bond_restr5.376323072
X-RAY DIFFRACTIONr_sphericity_free33.61751116
X-RAY DIFFRACTIONr_sphericity_bonded13.377523390
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A130590.04
12B130590.04
21A129120.03
22C129120.03
31A130190.03
32D130190.03
41B129460.04
42C129460.04
51B130660.04
52D130660.04
61C128870.03
62D128870.03
LS refinement shellResolution: 1.47→1.508 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 1084 -
Rwork0.346 19336 -
all-20420 -
obs--98.7 %

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