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- PDB-9hvr: Native glucuronoyl esterase OtCE15A from Opitutus terrae -

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Basic information

Entry
Database: PDB / ID: 9hvr
TitleNative glucuronoyl esterase OtCE15A from Opitutus terrae
ComponentsPutative acetyl xylan esterase
KeywordsHYDROLASE / Glucuronoyl 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: 1.392 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 glucuronoyl 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
DepositionJan 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1525
Polymers47,8451
Non-polymers3074
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-40 kcal/mol
Surface area14390 Å2
Unit cell
Length a, b, c (Å)50.382, 64.491, 117.121
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.18 Å3/Da / Density % sol: 43.49 %
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).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). Glycerol used as cryoprotectant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.39→58.561 Å / Num. obs: 63897 / % possible obs: 91.1 % / Redundancy: 8.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.027 / Rrim(I) all: 0.082 / Net I/σ(I): 14
Reflection shellResolution: 1.39→1.43 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3195 / CC1/2: 0.577 / Rpim(I) all: 0.428 / Rrim(I) all: 0.778 / % possible all: 43.9

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
REFMAC5.8.0430refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.392→58.561 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.071 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1697 3111 4.869 %
Rwork0.154 60786 -
all0.155 --
obs-63897 82.764 %
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: 15.369 Å2
Baniso -1Baniso -2Baniso -3
1--0.066 Å20 Å20 Å2
2--0.035 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.392→58.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 17 238 3300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123275
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162995
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.814485
X-RAY DIFFRACTIONr_angle_other_deg0.671.7646853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.868539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35710469
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.22110164
X-RAY DIFFRACTIONr_chiral_restr0.0990.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02843
X-RAY DIFFRACTIONr_nbd_refined0.2260.2706
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22838
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21595
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2198
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.210
X-RAY DIFFRACTIONr_nbd_other0.1820.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.219
X-RAY DIFFRACTIONr_mcbond_it1.4951.471623
X-RAY DIFFRACTIONr_mcbond_other1.4921.4691622
X-RAY DIFFRACTIONr_mcangle_it2.1972.642042
X-RAY DIFFRACTIONr_mcangle_other2.1962.642043
X-RAY DIFFRACTIONr_scbond_it2.6151.7371652
X-RAY DIFFRACTIONr_scbond_other2.4941.7261645
X-RAY DIFFRACTIONr_scangle_it3.8373.0542441
X-RAY DIFFRACTIONr_scangle_other3.8263.0382430
X-RAY DIFFRACTIONr_lrange_it4.6116.2453778
X-RAY DIFFRACTIONr_lrange_other4.59215.4693739
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
1.392-1.4280.273260.2725110.27256460.9490.9539.51120.275
1.428-1.4680.236610.24814320.24854940.9670.95827.17510.249
1.468-1.510.2361640.24128200.24153140.9580.9656.15360.237
1.51-1.5570.2291950.21838340.21852050.9650.96877.40630.21
1.557-1.6080.2092300.19543010.19650580.9720.97489.58090.186
1.608-1.6640.2112430.1845150.18148830.970.97997.44010.166
1.664-1.7270.192420.15644670.15747130.9760.98499.91510.14
1.727-1.7970.1812080.14843350.14945440.9810.98699.9780.132
1.797-1.8770.1742150.14341480.14443630.9810.9871000.13
1.877-1.9680.1782080.14639620.14741700.9810.9871000.135
1.968-2.0750.1692030.1537760.15139810.9820.98699.94980.143
2.075-2.20.1821940.14635930.14737880.9770.98799.97360.142
2.2-2.3520.1751690.14633740.14835460.9820.98799.91540.147
2.352-2.540.1521570.14131630.14133200.9850.9881000.144
2.54-2.7820.1911210.14529530.14630740.9750.9871000.154
2.782-3.110.161420.15126570.15128000.9850.98699.96430.167
3.11-3.5890.1391070.14923740.14924820.9870.98799.95970.172
3.589-4.3920.145910.12820210.12921120.9880.991000.16
4.392-6.1930.144820.15116040.15116870.9890.98999.94070.194
6.193-58.5610.152530.29460.19710010.9840.97799.80020.253

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