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- PDB-9huc: The glucuronyl esterase OtCE15A from Opitutus terrae in complex w... -

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Basic information

Entry
Database: PDB / ID: 9huc
TitleThe glucuronyl esterase OtCE15A from Opitutus terrae in complex with a heptasaccharide
ComponentsPutative acetyl xylan esterase
KeywordsHYDROLASE / Glucuroyl esterase / Opitutus terrae / Lignocellulose / Carbohydrate
Function / homology: / Glucuronyl esterase, fungi / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae PB90-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsOestberg, E.B. / Lo Leggio, L. / Zaghini, A. / Mazurkewich, S. / Larsbrink, J.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF21OC0071611 Denmark
CitationJournal: To Be Published
Title: Interaction of a glucuronyl esterase with complex fragments of the plant cell wall
Authors: Zaghini, A. / Oestberg, E.B. / Banerjee, S. / Mazurkewich, S. / Yu, L. / Dupree, P. / Larsbrink, J. / Lo Leggio, L.
History
DepositionDec 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8693
Polymers47,8451
Non-polymers1,0242
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-9 kcal/mol
Surface area14520 Å2
Unit cell
Length a, b, c (Å)50.770, 65.430, 118.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative acetyl xylan esterase


Mass: 47844.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opitutus terrae PB90-1 (bacteria) / Gene: Oter_0116 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1ZMF4
#2: Polysaccharide alpha-L-arabinofuranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D- ...alpha-L-arabinofuranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 1000.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,7,6/[a212h-1b_1-5][a2122A-1a_1-5_4*OC][a211h-1a_1-4]/1-1-2-1-1-3-1/a4-b1_b2-c1_b4-d1_d4-e1_e3-f1_e4-g1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(3+1)][a-L-Araf]{}[(4+1)][b-D-Xylp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: OtCE15A mixed 3:1 with reservoir containing 0.10 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate ...Details: OtCE15A mixed 3:1 with reservoir containing 0.10 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1 M Buffer system 1, pH 6.5 (Imidazole; MES monohydrate (acid)), 37.50 % v/v, Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350). Solid oligosaccharide added to the drop and soaked for 15 min.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03285 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03285 Å / Relative weight: 1
ReflectionResolution: 2.4→38.6 Å / Num. obs: 14772 / % possible obs: 92.3 % / Redundancy: 4.567 % / CC1/2: 0.993 / Rrim(I) all: 0.184 / Net I/σ(I): 11.15
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 3.59 % / Mean I/σ(I) obs: 2.42 / Num. unique obs: 898 / CC1/2: 0.786 / Rrim(I) all: 0.718 / % possible all: 78

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.403→38.599 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.9 / SU B: 10.239 / SU ML: 0.231 / Cross valid method: FREE R-VALUE / ESU R: 0.832 / ESU R Free: 0.299
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2451 761 5.152 %
Rwork0.1676 14011 -
all0.172 --
obs-14772 92.244 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.295 Å2
Baniso -1Baniso -2Baniso -3
1--1.981 Å2-0 Å20 Å2
2--2.421 Å2-0 Å2
3----0.441 Å2
Refinement stepCycle: LAST / Resolution: 2.403→38.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 69 119 3243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123274
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162970
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.6614490
X-RAY DIFFRACTIONr_angle_other_deg0.4731.5766818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0925406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.174536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78110454
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.30510160
X-RAY DIFFRACTIONr_chiral_restr0.0690.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02814
X-RAY DIFFRACTIONr_nbd_refined0.210.2733
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.22791
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21601
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21614
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2153
X-RAY DIFFRACTIONr_metal_ion_refined0.1620.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0470.25
X-RAY DIFFRACTIONr_nbd_other0.170.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.24
X-RAY DIFFRACTIONr_mcbond_it2.1713.5071600
X-RAY DIFFRACTIONr_mcbond_other2.173.5081600
X-RAY DIFFRACTIONr_mcangle_it3.4136.2972005
X-RAY DIFFRACTIONr_mcangle_other3.4176.32006
X-RAY DIFFRACTIONr_scbond_it2.6273.9081674
X-RAY DIFFRACTIONr_scbond_other2.6263.9121675
X-RAY DIFFRACTIONr_scangle_it4.2497.062483
X-RAY DIFFRACTIONr_scangle_other4.2497.0642484
X-RAY DIFFRACTIONr_lrange_it5.8434.4273746
X-RAY DIFFRACTIONr_lrange_other5.84334.2793734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.403-2.4650.359530.2458390.25211440.9040.95777.9720.222
2.465-2.5330.294470.2199030.22211540.9360.96682.32240.189
2.533-2.6060.222510.1968510.19710860.9670.97383.05710.166
2.606-2.6850.304380.1888790.19310790.9560.97484.98610.156
2.685-2.7730.315380.2038510.20810200.9370.9787.15690.166
2.773-2.870.247490.1978620.210190.9590.97289.40140.162
2.87-2.9780.316560.2048370.2119650.9070.96892.53890.168
2.978-3.0980.307380.1918390.1959240.9440.97194.91340.154
3.098-3.2350.355490.1748490.1829050.9230.97899.22650.144
3.235-3.3920.226470.1668250.1698750.9720.9899.65710.138
3.392-3.5740.242370.1727660.1758090.9530.97699.25830.145
3.574-3.7890.251460.1777310.1817870.9520.97898.72940.152
3.789-4.0470.211270.1756960.1767380.9650.97697.96750.152
4.047-4.3680.242300.1376680.1417070.9670.98898.7270.124
4.368-4.7780.18370.1295810.1336210.9760.98999.51690.119
4.778-5.3320.176370.1285490.1315890.9810.98999.49070.118
5.332-6.1380.22240.1335060.1375330.9770.9999.43710.124
6.138-7.470.203280.1484230.1524540.9720.98799.33920.137
7.47-10.3720.278160.1243420.1293670.9550.99197.54770.126
10.372-38.5990.201130.1872150.1882340.990.97897.43590.199

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