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- PDB-12oa: Crystal structure of a GH26 enzyme (EiGH26c) -

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Basic information

Entry
Database: PDB / ID: 12oa
TitleCrystal structure of a GH26 enzyme (EiGH26c)
ComponentsGlycoside hydrolase family 26
KeywordsHYDROLASE / metagenome / manatee / gut microbiota / heteromannan
Function / homologyTRIETHYLENE GLYCOL
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsMiyamoto, R.Y. / Araujo, E.A. / Noske, G.D. / Oliveira, C.H.M. / Martins, M.P. / Murakami, M.T.
Funding support Brazil, 5items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/04891-3 Brazil
Sao Paulo Research Foundation (FAPESP)2022/03059-5 Brazil
Sao Paulo Research Foundation (FAPESP)2021/09793-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303898/2024-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)304440/2024-8 Brazil
CitationJournal: To Be Published
Title: Crystal structure of a GH26 enzyme (EiGH26c)
Authors: Persinoti, G.F. / Martins, M.P. / Silva, C.B.C. / Streit, R.S.A. / Paixao, D.A.A. / Martins, G.H. / Higasi, P.M.R. / Braatz, G.M. / Silva, M.K.P. / Morao, L.G. / Martins-Junior, J. / ...Authors: Persinoti, G.F. / Martins, M.P. / Silva, C.B.C. / Streit, R.S.A. / Paixao, D.A.A. / Martins, G.H. / Higasi, P.M.R. / Braatz, G.M. / Silva, M.K.P. / Morao, L.G. / Martins-Junior, J. / Stoffel, F. / Ciol, H. / Noske, G.D. / Miyamoto, R.Y. / Oliveira, G.M. / Martim, D.B. / Oliveira, C.H.M. / Almeida, O.A.C. / Araujo, E.A. / Andrade, M.O. / Santos, C.A. / Diogo, J.A. / Wolf, L.D. / Zanotto, J.V. / Souza, A.R. / Goncalves, F.A.C. / Mello, D.M.D. / Morais, M.A.B. / Porto, J. / Lombard, V. / Giuseppe, P.O. / Terrapon, N. / Lemos, L.N. / Henrissat, B. / Carvalho, V.L. / Silva, V.M.F. / Murakami, M.T.
History
DepositionApr 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 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: Glycoside hydrolase family 26
B: Glycoside hydrolase family 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,16510
Polymers86,3812
Non-polymers7858
Water10,215567
1
A: Glycoside hydrolase family 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5565
Polymers43,1901
Non-polymers3654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6105
Polymers43,1901
Non-polymers4194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.468, 210.750, 63.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glycoside hydrolase family 26


Mass: 43190.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.77→46.12 Å / Num. obs: 179637 / % possible obs: 47.2 % / Redundancy: 6.777 % / CC1/2: 0.993 / Rmerge(I) obs: 0.139 / Rrim(I) all: 0.182 / Net I/σ(I): 3.84
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.77-1.873.085138090.0854.1191
1.87-21.657129270.2542.1991
2-2.160.887125750.561.1581
2.16-2.370.584115030.7530.7531
2.37-2.650.36899870.8570.4751
2.65-3.050.17885940.9570.2321
3.05-3.740.08572440.9890.111
3.74-5.270.04850980.9920.0651
5.27-46.120.02831470.9980.0361

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→46.12 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 4696 5 %
Rwork0.1806 --
obs0.1822 93894 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 47 567 6496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016097
X-RAY DIFFRACTIONf_angle_d1.0118276
X-RAY DIFFRACTIONf_dihedral_angle_d12.2032159
X-RAY DIFFRACTIONf_chiral_restr0.058850
X-RAY DIFFRACTIONf_plane_restr0.0091060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.790.38641490.3852829X-RAY DIFFRACTION97
1.79-1.810.361550.3272943X-RAY DIFFRACTION100
1.81-1.830.33691550.31152932X-RAY DIFFRACTION100
1.83-1.850.3441560.3052963X-RAY DIFFRACTION100
1.85-1.880.29891520.29032904X-RAY DIFFRACTION100
1.88-1.90.39231570.29932968X-RAY DIFFRACTION100
1.9-1.930.33121540.27592924X-RAY DIFFRACTION100
1.93-1.960.28491550.25822941X-RAY DIFFRACTION100
1.96-1.990.25371550.23392952X-RAY DIFFRACTION100
1.99-2.020.28161560.2082966X-RAY DIFFRACTION100
2.02-2.060.25011550.20382951X-RAY DIFFRACTION100
2.06-2.090.23721530.18782901X-RAY DIFFRACTION100
2.09-2.130.23441560.18672966X-RAY DIFFRACTION100
2.13-2.180.21011560.18242953X-RAY DIFFRACTION100
2.18-2.230.23381550.17222948X-RAY DIFFRACTION100
2.23-2.280.20661570.17382996X-RAY DIFFRACTION100
2.28-2.330.22411550.17272930X-RAY DIFFRACTION100
2.33-2.40.22841560.17322961X-RAY DIFFRACTION100
2.4-2.470.21551560.16632981X-RAY DIFFRACTION100
2.47-2.550.21721560.17082959X-RAY DIFFRACTION100
2.55-2.640.21511580.17682991X-RAY DIFFRACTION100
2.64-2.740.221550.17022954X-RAY DIFFRACTION100
2.74-2.870.17861580.18532995X-RAY DIFFRACTION100
2.87-3.020.23811570.19562985X-RAY DIFFRACTION100
3.02-3.210.21911590.18773023X-RAY DIFFRACTION100
3.21-3.460.20241570.16812985X-RAY DIFFRACTION100
3.46-3.80.16611600.15163039X-RAY DIFFRACTION100
3.81-4.350.16121600.13383037X-RAY DIFFRACTION100
4.36-5.490.15841620.1513083X-RAY DIFFRACTION100
5.49-46.120.2081710.1873238X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.59250.6897-0.22621.2376-0.05180.45320.0516-0.0725-0.1006-0.0016-0.05310.0509-0.02240.0344-0.00740.34810.05640.02020.24450.00640.2451-21.797120.7333-9.0955
20.97850.2974-0.11571.404-0.311.7495-0.1003-0.0063-0.0712-0.08050.0258-0.1506-0.03980.10040.07140.2104-0.01920.02710.1866-0.01580.212410.195236.534121.7778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 116 through 484)
2X-RAY DIFFRACTION2(chain 'B' and resid 118 through 484)

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