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- PDB-7p1u: Structure of KDNase from Trichophyton Rubrum in complex with 2-ke... -

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Basic information

Entry
Database: PDB / ID: 7p1u
TitleStructure of KDNase from Trichophyton Rubrum in complex with 2-keto-3-deoxynononic acid
ComponentsExtracellular sialidase/neuraminidase
KeywordsCARBOHYDRATE / Carbohydrate Metabolism / Enzyme Structure / Protein Structure / KDN / KDNase / Sialic Acid / Sialidase
Function / homologyBNR repeat-like domain / exo-alpha-sialidase activity / Sialidase family / Sialidase / Sialidase superfamily / deamino-alpha-neuraminic acid / Extracellular sialidase/neuraminidase
Function and homology information
Biological speciesTrichophyton rubrum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 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 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,1516
Polymers84,4302
Non-polymers7214
Water16,069892
1
A: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5753
Polymers42,2151
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5753
Polymers42,2151
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.450, 74.010, 160.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 386
2010B4 - 386

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Components

#1: Protein Extracellular sialidase/neuraminidase


Mass: 42214.945 Da / Num. of mol.: 2
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-KDM / deamino-alpha-neuraminic acid / alpha-deaminoneuraminic acid / 3-deoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid / sialic acid / (2R,4S,5R,6R)-2,4,5-TRIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]OXANE-2-CARBOXYLIC-ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 268.218 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C9H16O9
IdentifierTypeProgram
DKdnpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
2-keto-3-deoxy-a-D-nonulopyranosic acidCOMMON NAMEGMML 1.0
a-D-KdnpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdnSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% Peg 3350, 0.2m K formate

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 0.99→47.73 Å / Num. obs: 405311 / % possible obs: 98.5 % / Redundancy: 5.4 % / CC1/2: 0.999 / Net I/σ(I): 8.9
Reflection shellResolution: 0.99→1.01 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 1 / Num. unique obs: 18293 / CC1/2: 0.7 / % possible all: 89.6

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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: 0.99→47.73 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.158 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 19946 4.9 %RANDOM
Rwork0.218 ---
obs0.2192 385221 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 192.06 Å2 / Biso mean: 12.478 Å2 / Biso min: 5.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---0.69 Å20 Å2
3---0.42 Å2
Refinement stepCycle: final / Resolution: 0.99→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5857 0 48 900 6805
Biso mean--11.18 27.88 -
Num. residues----766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196297
X-RAY DIFFRACTIONr_bond_other_d0.0060.025626
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9458585
X-RAY DIFFRACTIONr_angle_other_deg0.852.99413101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1645824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26323.165278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.097151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4411558
X-RAY DIFFRACTIONr_chiral_restr0.1010.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217270
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021332
X-RAY DIFFRACTIONr_rigid_bond_restr5.798311923
X-RAY DIFFRACTIONr_sphericity_free24.2285531
X-RAY DIFFRACTIONr_sphericity_bonded15.034512128
Refine LS restraints NCS

Ens-ID: 1 / Number: 14069 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 0.99→1.016 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 1366 -
Rwork0.49 26148 -
all-27514 -
obs--91.16 %

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