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- PDB-7p1s: Structure of KDNase from Trichophyton Rubrum in complex with 2,3-... -

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Basic information

Entry
Database: PDB / ID: 7p1s
TitleStructure of KDNase from Trichophyton Rubrum in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.
ComponentsExtracellular sialidase/neuraminidase
KeywordsCARBOHYDRATE / Carbohydrate Metabolism / Enzyme Structure / Protein Structure / KDN / KDNase / Sialic Acid / Sialidase
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / metal ion binding / membrane / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
Chem-KFN / exo-alpha-sialidase
Similarity search - Component
Biological speciesTrichophyton rubrum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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)169,95312
Polymers168,8604
Non-polymers1,0938
Water13,799766
1
A: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4883
Polymers42,2151
Non-polymers2732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4883
Polymers42,2151
Non-polymers2732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4883
Polymers42,2151
Non-polymers2732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4883
Polymers42,2151
Non-polymers2732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.646, 179.008, 97.292
Angle α, β, γ (deg.)90.000, 104.040, 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
1010A5 - 383
2010B5 - 383
1020A5 - 383
2020C5 - 383
1030A5 - 383
2030D5 - 383
1040B4 - 384
2040C4 - 384
1050B4 - 384
2050D4 - 384
1060C4 - 384
2060D4 - 384

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Extracellular sialidase/neuraminidase


Mass: 42214.945 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: 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.: 4 / Source method: obtained synthetically / Formula: C9H14O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 25% PEG 1500 0.1M SPG pH 8

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 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: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.92→179.01 Å / Num. obs: 113657 / % possible obs: 92.5 % / Redundancy: 2.9 % / CC1/2: 0.97 / Rmerge(I) obs: 0.145 / Net I/σ(I): 4.6
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4982 / CC1/2: 0.49 / % possible all: 55.1

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Processing

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

2xcy


Resolution: 1.92→179.01 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.704 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 5690 5 %RANDOM
Rwork0.2598 ---
obs0.2612 107924 92.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.97 Å2 / Biso mean: 31.141 Å2 / Biso min: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20.46 Å2
2--0.97 Å20 Å2
3----1.21 Å2
Refinement stepCycle: final / Resolution: 1.92→179.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11688 0 72 766 12526
Biso mean--24.59 29.47 -
Num. residues----1523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912035
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210790
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.94916318
X-RAY DIFFRACTIONr_angle_other_deg0.747325077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9351519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93523.26546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.808151916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.52115108
X-RAY DIFFRACTIONr_chiral_restr0.0740.21723
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022528
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A128570.05
12B128570.05
21A128350.05
22C128350.05
31A128050.05
32D128050.05
41B129730.05
42C129730.05
51B129170.05
52D129170.05
61C129540.04
62D129540.04
LS refinement shellResolution: 1.92→1.968 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.377 251 -
Rwork0.36 4729 -
obs--54.99 %

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