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- PDB-7p1r: Structure of Trichophyton Rubrum KDNase in complex with 2,3-diflu... -

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Basic information

Entry
Database: PDB / ID: 7p1r
TitleStructure of Trichophyton Rubrum KDNase in complex with 2,3-difluoro-KDN
ComponentsExtracellular sialidase/neuraminidase
KeywordsCARBOHYDRATE / Carbohydrate Metabolism / Enzyme Structure / Protein Structure / KDN / KDNase / Sialic Acid / Sialidase / Trichophyton rubrum
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / metal ion binding / membrane / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
Chem-FKD / PHOSPHATE ION / Extracellular sialidase/neuraminidase
Similarity search - Component
Biological speciesTrichophyton rubrum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
Revision 1.3Nov 6, 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

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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)170,85620
Polymers168,8604
Non-polymers1,99716
Water33,9221883
1
A: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7145
Polymers42,2151
Non-polymers4994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7145
Polymers42,2151
Non-polymers4994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7145
Polymers42,2151
Non-polymers4994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7145
Polymers42,2151
Non-polymers4994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.910, 179.490, 98.070
Angle α, β, γ (deg.)90.000, 103.890, 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
1010A4 - 385
2010B4 - 385
1020A4 - 384
2020C4 - 384
1030A4 - 384
2030D4 - 384
1040B4 - 384
2040C4 - 384
1050B4 - 384
2050D4 - 384
1060C4 - 386
2060D4 - 386

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: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#4: 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.: 4 / Source method: obtained synthetically / Formula: C9H15FO9 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1883 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 25% PEG 1500, 0.1M SPG pH4

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Data collection

DiffractionMean temperature: 80 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: 1.75→95.2 Å / Num. obs: 158507 / % possible obs: 96.6 % / Redundancy: 2.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 7614 / CC1/2: 0.712 / % possible all: 94.5

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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: 1.75→95.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.774 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 7944 5 %RANDOM
Rwork0.1838 ---
obs0.1853 150514 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.76 Å2 / Biso mean: 23.655 Å2 / Biso min: 10.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.11 Å2
2--0.42 Å20 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.75→95.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11739 0 116 1889 13744
Biso mean--27.2 33.79 -
Num. residues----1530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01912176
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210845
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.95316529
X-RAY DIFFRACTIONr_angle_other_deg0.782325221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85351540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78523.369555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.639151926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.72815108
X-RAY DIFFRACTIONr_chiral_restr0.0870.21748
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022537
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A129700.06
12B129700.06
21A128820.05
22C128820.05
31A129090.06
32D129090.06
41B129300.06
42C129300.06
51B130570.04
52D130570.04
61C129860.06
62D129860.06
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 551 -
Rwork0.253 10840 -
all-11391 -
obs--94.21 %

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