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- PDB-6mrx: Sialidase26 apo -

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Basic information

Entry
Database: PDB / ID: 6mrx
TitleSialidase26 apo
ComponentsSialidase26
KeywordsHYDROLASE / Sialidase / microbiome / Neu5Ac / sialic acid / inflammation
Function / homology
Function and homology information


exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / intracellular membrane-bounded organelle / membrane / cytoplasm
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
Biological speciesunidentified bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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. / Chang, G. ...Zaramela, L.S. / Martino, C. / Alisson-Silva, F. / Rees, S.D. / Diaz, S.L. / Chuzel, L. / Ganatra, M.B. / Taron, C.H. / Zuniga, C. / 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
DepositionOct 15, 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 1.4Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)246,8324
Polymers246,8324
Non-polymers00
Water5,080282
1
A: Sialidase26
B: Sialidase26


Theoretical massNumber of molelcules
Total (without water)123,4162
Polymers123,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-12 kcal/mol
Surface area37520 Å2
MethodPISA
2
C: Sialidase26
D: Sialidase26


Theoretical massNumber of molelcules
Total (without water)123,4162
Polymers123,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-12 kcal/mol
Surface area37570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.476, 79.817, 260.811
Angle α, β, γ (deg.)90.000, 100.918, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPSERSER(chain 'A' and (resid 23 through 53 or resid 55 through 543))AA23 - 5323 - 53
12THRTHRLYSLYS(chain 'A' and (resid 23 through 53 or resid 55 through 543))AA55 - 54355 - 543
21ASPASPSERSER(chain 'B' and (resid 23 through 53 or resid 55 through 543))BB23 - 5323 - 53
22THRTHRLYSLYS(chain 'B' and (resid 23 through 53 or resid 55 through 543))BB55 - 54355 - 543
31ASPASPSERSER(chain 'C' and (resid 23 through 53 or resid 55 through 543))CC23 - 5323 - 53
32THRTHRLYSLYS(chain 'C' and (resid 23 through 53 or resid 55 through 543))CC55 - 54355 - 543
41ASPASPSERSER(chain 'D' and (resid 23 through 53 or resid 55 through 543))DD23 - 5323 - 53
42THRTHRLYSLYS(chain 'D' and (resid 23 through 53 or resid 55 through 543))DD55 - 54355 - 543

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Components

#1: Protein
Sialidase26


Mass: 61708.102 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
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: 8.2.2 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2→48.42 Å / Num. obs: 157373 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.37 Å2 / Net I/σ(I): 6.9
Reflection shellResolution: 2→2.03 Å

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q6K

4q6k


Resolution: 2→48.42 Å / SU ML: 0.2605 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 27.2855
RfactorNum. reflection% reflection
Rfree0.2415 15073 5.02 %
Rwork0.2244 --
obs0.2253 157315 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.2 Å2
Refinement stepCycle: LAST / Resolution: 2→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16270 0 0 282 16552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002416630
X-RAY DIFFRACTIONf_angle_d0.590722566
X-RAY DIFFRACTIONf_chiral_restr0.04752536
X-RAY DIFFRACTIONf_plane_restr0.0032898
X-RAY DIFFRACTIONf_dihedral_angle_d10.37419958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.32755040.31669110X-RAY DIFFRACTION93.89
2.02-2.050.34854390.3129232X-RAY DIFFRACTION93.67
2.05-2.070.33734710.30879224X-RAY DIFFRACTION94.48
2.07-2.10.33194640.30889357X-RAY DIFFRACTION94.19
2.1-2.130.32845220.30519172X-RAY DIFFRACTION95.03
2.13-2.150.31955010.29789289X-RAY DIFFRACTION94.91
2.15-2.190.31284790.29839324X-RAY DIFFRACTION95.66
2.19-2.220.31564890.28329490X-RAY DIFFRACTION95.62
2.22-2.250.29684880.29159327X-RAY DIFFRACTION96.56
2.25-2.290.28215210.28179387X-RAY DIFFRACTION96.26
2.29-2.330.30755000.28169471X-RAY DIFFRACTION96.85
2.33-2.370.31625050.27869448X-RAY DIFFRACTION96.59
2.37-2.420.27625020.26959602X-RAY DIFFRACTION97.09
2.42-2.470.29325220.27399479X-RAY DIFFRACTION97.33
2.47-2.520.2944900.26379477X-RAY DIFFRACTION97.29
2.52-2.580.30255110.26539514X-RAY DIFFRACTION97.59
2.58-2.640.31365030.26559562X-RAY DIFFRACTION97.86
2.64-2.710.27235170.26149581X-RAY DIFFRACTION97.7
2.71-2.790.27135160.25999531X-RAY DIFFRACTION98.19
2.79-2.880.29115240.25869679X-RAY DIFFRACTION98.31
2.88-2.990.25674760.24979677X-RAY DIFFRACTION98.5
2.99-3.110.26465150.24389585X-RAY DIFFRACTION98.71
3.11-3.250.26544890.2459668X-RAY DIFFRACTION98.75
3.25-3.420.22654620.22179756X-RAY DIFFRACTION98.91
3.42-3.630.22595430.20599715X-RAY DIFFRACTION99.12
3.63-3.910.20174630.1869693X-RAY DIFFRACTION99.23
3.91-4.310.17835290.1599697X-RAY DIFFRACTION99.26
4.31-4.930.1395490.13269734X-RAY DIFFRACTION99.39
4.93-6.210.15685530.14479697X-RAY DIFFRACTION99.75
6.21-48.430.19585260.15819758X-RAY DIFFRACTION99.77

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