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- PDB-9ega: Crystal Structure of a CE20 carbohydrate acetylesterase from Pedo... -

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Basic information

Entry
Database: PDB / ID: 9ega
TitleCrystal Structure of a CE20 carbohydrate acetylesterase from Pedobacter psychrotolerans (PpCE20_II), with ancillary domain
ComponentsSialate O-acetylesterase
KeywordsHYDROLASE / Esterase / Carbohydrate / Polysaccharide / Multimodular
Function / homology
Function and homology information


sialate O-acetylesterase activity / carbohydrate metabolic process
Similarity search - Function
Sialate O-acetylesterase / Sialate O-acetylesterase domain / Carbohydrate esterase, sialic acid-specific acetylesterase / SGNH hydrolase superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / phenylmethanesulfonic acid / Sialate O-acetylesterase
Similarity search - Component
Biological speciesPedobacter psychrotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsVieira, P.S. / Morais, M.A.B. / Murakami, M.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)16/06509-0 Brazil
Sao Paulo Research Foundation (FAPESP)15/26982-0 Brazil
CitationJournal: Nat Commun / Year: 2025
Title: Insights into a water-mediated catalytic triad architecture in CE20 carbohydrate esterases.
Authors: Teune, M. / Vieira, P.S. / Dohler, T. / Palm, G.J. / Dutschei, T. / Bartosik, D. / Berndt, L. / Persinoti, G.F. / Maass, S. / Becher, D. / Schweder, T. / Murakami, M.T. / Lammers, M. / Bornscheuer, U.T.
History
DepositionNov 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialate O-acetylesterase
B: Sialate O-acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8057
Polymers145,2622
Non-polymers5435
Water33,0761836
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.134, 125.135, 108.688
Angle α, β, γ (deg.)90.00, 104.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sialate O-acetylesterase


Mass: 72630.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PMSF-covalently modified Expressed construction starts at residue number 24 from original primary sequence
Source: (gene. exp.) Pedobacter psychrotolerans (bacteria) / Gene: EV200_102244 / Production host: Escherichia coli (E. coli) / Variant (production host): SHuffle / References: UniProt: A0A4R2HIK5
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H8O3S / Source: (gene. exp.) Pedobacter psychrotolerans (bacteria) / Gene: EV200_102244 / Production host: Escherichia coli (E. coli) / Variant (production host): SHuffle
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1836 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.55 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 150 mmol/L DL-malate dissodic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 314320 / % possible obs: 99.2 % / Redundancy: 6.69 % / CC1/2: 0.999 / Net I/σ(I): 12.64
Reflection shellResolution: 1.35→1.43 Å / Mean I/σ(I) obs: 1.27 / Num. unique obs: 48928 / CC1/2: 0.599

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→49.72 Å / Cross valid method: FREE R-VALUE / σ(F): 34.85 / Phase error: 22.1 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1918 15779 5.02 %
Rwork0.1589 --
obs0.1658 314310 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9960 0 32 1836 11828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510326
X-RAY DIFFRACTIONf_angle_d0.80314015
X-RAY DIFFRACTIONf_dihedral_angle_d14.173846
X-RAY DIFFRACTIONf_chiral_restr0.0841468
X-RAY DIFFRACTIONf_plane_restr0.0051813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.33917400.325214053X-RAY DIFFRACTION89
1.37-1.40.33287560.29314367X-RAY DIFFRACTION91
1.4-1.430.28437670.26814570X-RAY DIFFRACTION92
1.43-1.450.26847800.253114828X-RAY DIFFRACTION94
1.45-1.490.25857880.23514975X-RAY DIFFRACTION95
1.49-1.520.22327930.22515055X-RAY DIFFRACTION95
1.52-1.560.20787920.208115056X-RAY DIFFRACTION95
1.56-1.60.22457900.202515012X-RAY DIFFRACTION95
1.6-1.650.22337890.193214990X-RAY DIFFRACTION95
1.65-1.70.21527920.19315050X-RAY DIFFRACTION95
1.7-1.760.20487900.184714999X-RAY DIFFRACTION95
1.76-1.830.20247880.18114969X-RAY DIFFRACTION95
1.83-1.920.19827910.176415035X-RAY DIFFRACTION95
1.92-2.020.19787960.176615125X-RAY DIFFRACTION95
2.02-2.140.19587900.175815010X-RAY DIFFRACTION95
2.14-2.310.19057910.170215037X-RAY DIFFRACTION95
2.31-2.540.19297950.169515093X-RAY DIFFRACTION95
2.54-2.910.19717920.156915048X-RAY DIFFRACTION95
2.91-3.660.18997930.139415067X-RAY DIFFRACTION95
3.66-49.720.15868030.114815255X-RAY DIFFRACTION95

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