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- PDB-6myv: Sialidase26 co-crystallized with DANA-Gc -

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Basic information

Entry
Database: PDB / ID: 6myv
TitleSialidase26 co-crystallized with DANA-Gc
ComponentsSialidase26
KeywordsHYDROLASE / Sialidase / microbiome / Neu5Gc / sialic acid / inflammation / Neu5Gc2en / DANA / DANA-Gc / Gc
Function / homology
Function and homology information


exo-alpha-sialidase activity
Similarity search - Function
Sialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / Immunoglobulin-like - #1290 / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase ...Sialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / Immunoglobulin-like - #1290 / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-GC9 / Sialidase
Similarity search - Component
Biological speciesunidentified bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZaramela, L.S. / Martino, C. / Alisson-Silva, F. / Rees, S.D. / Diaz, S.L. / Chuzel, L. / Ganatra, M.B. / Taron, C.H. / Zuniga, C. / Huang, J. ...Zaramela, L.S. / Martino, C. / Alisson-Silva, F. / Rees, S.D. / Diaz, S.L. / Chuzel, L. / Ganatra, M.B. / Taron, C.H. / Zuniga, C. / Huang, J. / Siegel, D. / Chang, G. / Varki, A. / Zengler, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1444435 United States
Citation
Journal: Nat Microbiol / Year: 2019
Title: Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates.
Authors: Zaramela, L.S. / Martino, C. / Alisson-Silva, F. / Rees, S.D. / Diaz, S.L. / Chuzel, L. / Ganatra, M.B. / Taron, C.H. / Secrest, P. / Zuniga, C. / Huang, J. / Siegel, D. / Chang, G. / Varki, A. / Zengler, K.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionNov 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Apr 22, 2020Group: Atomic model / Data collection / Category: atom_site / chem_comp
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.mon_nstd_flag / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialidase26
B: Sialidase26
C: Sialidase26
D: Sialidase26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,0748
Polymers233,8454
Non-polymers1,2294
Water14,196788
1
A: Sialidase26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7682
Polymers58,4611
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sialidase26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7682
Polymers58,4611
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sialidase26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7682
Polymers58,4611
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sialidase26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7682
Polymers58,4611
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.645, 89.753, 95.806
Angle α, β, γ (deg.)64.700, 75.650, 88.580
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 22 through 516 or (resid 517...
21(chain B and (resid 22 through 516 or (resid 517...
31(chain C and (resid 22 through 516 or (resid 517...
41chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 22 through 516 or (resid 517...A22 - 516
121(chain A and (resid 22 through 516 or (resid 517...A517
131(chain A and (resid 22 through 516 or (resid 517...A22 - 582
141(chain A and (resid 22 through 516 or (resid 517...A22 - 582
151(chain A and (resid 22 through 516 or (resid 517...A22 - 582
161(chain A and (resid 22 through 516 or (resid 517...A22 - 582
211(chain B and (resid 22 through 516 or (resid 517...B22 - 516
221(chain B and (resid 22 through 516 or (resid 517...B517
231(chain B and (resid 22 through 516 or (resid 517...B22 - 582
241(chain B and (resid 22 through 516 or (resid 517...B22 - 582
251(chain B and (resid 22 through 516 or (resid 517...B22 - 582
261(chain B and (resid 22 through 516 or (resid 517...B22 - 582
311(chain C and (resid 22 through 516 or (resid 517...C22 - 516
321(chain C and (resid 22 through 516 or (resid 517...C517
331(chain C and (resid 22 through 516 or (resid 517...C22 - 582
341(chain C and (resid 22 through 516 or (resid 517...C22 - 582
351(chain C and (resid 22 through 516 or (resid 517...C22 - 582
361(chain C and (resid 22 through 516 or (resid 517...C22 - 582
411chain DD22 - 582

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Components

#1: Protein
Sialidase26


Mass: 58461.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified bacterium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4S2B4D9*PLUS
#2: Sugar
ChemComp-GC9 / 2,6-anhydro-3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-L-altro-non-2-enonic acid


Type: L-saccharide / Mass: 307.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H17NO9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 788 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 6000, 0.1 M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.2→48.5 Å / Num. obs: 126317 / % possible obs: 98.3 % / Redundancy: 3.9 % / Net I/σ(I): 6
Reflection shellResolution: 2.2→2.24 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q6K

4q6k


Resolution: 2.2→48.5 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2612 6258 5.05 %
Rwork0.2305 117649 -
obs0.232 123907 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.12 Å2 / Biso mean: 34.1178 Å2 / Biso min: 14.28 Å2
Refinement stepCycle: final / Resolution: 2.2→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16312 0 84 788 17184
Biso mean--38.2 33.65 -
Num. residues----2092
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10245X-RAY DIFFRACTION6.682TORSIONAL
12B10245X-RAY DIFFRACTION6.682TORSIONAL
13C10245X-RAY DIFFRACTION6.682TORSIONAL
14D10245X-RAY DIFFRACTION6.682TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2250.31542100.30033869407997
2.225-2.25120.3292140.29723859407397
2.2512-2.27860.37931810.30193973415498
2.2786-2.30750.34072160.30093867408397
2.3075-2.33780.32732070.28933856406398
2.3378-2.36990.29272020.28143982418497
2.3699-2.40370.35382310.28333783401498
2.4037-2.43960.2852060.28213931413798
2.4396-2.47770.29212250.27033921414698
2.4777-2.51830.29462110.27263874408598
2.5183-2.56180.30112110.26123904411597
2.5618-2.60830.291800.26713932411298
2.6083-2.65850.31262160.26923903411998
2.6585-2.71280.30452280.26273888411698
2.7128-2.77170.2991890.25893952414198
2.7717-2.83620.30841970.25063942413998
2.8362-2.90710.26312060.24083921412798
2.9071-2.98570.26752210.2463911413298
2.9857-3.07360.31892010.2463952415398
3.0736-3.17280.27672090.24553914412398
3.1728-3.28610.27512100.23183928413898
3.2861-3.41770.24412100.22273969417999
3.4177-3.57320.25972010.22413921412298
3.5732-3.76150.25552370.21673880411799
3.7615-3.9970.2422020.20424006420899
3.997-4.30550.20751950.19173956415199
4.3055-4.73840.18742060.17863960416699
4.7384-5.42330.20192240.18273932415699
5.4233-6.82980.23712060.20553995420199
6.8298-48.51140.22892060.21133968417499

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