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- PDB-12nw: Crystal structure of a GH26 enzyme (EiGH26a) in complex with galactose -

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Basic information

Entry
Database: PDB / ID: 12nw
TitleCrystal structure of a GH26 enzyme (EiGH26a) in complex with galactose
ComponentsGlycoside hydrolase family 26
KeywordsHYDROLASE / metagenome / manatee / gut microbiota / heteromannan
Function / homologybeta-D-galactopyranose / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsMiyamoto, R.Y. / Oliveira, C.H.M. / Morao, L.G. / 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 (EiGH26a) in complex with galactose
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7835
Polymers39,3061
Non-polymers4774
Water3,099172
1
A: Glycoside hydrolase family 26
hetero molecules

A: Glycoside hydrolase family 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,56610
Polymers78,6132
Non-polymers9548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3710 Å2
ΔGint1 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.775, 65.328, 84.029
Angle α, β, γ (deg.)90.00, 110.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glycoside hydrolase family 26


Mass: 39306.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 175 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M magnesium chloride hexahydrate; 0.1M tris hydrochloride pH 8.5; 30% (w/v) PEG 4000

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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: Dec 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.53→45.2 Å / Num. obs: 51075 / % possible obs: 40.9 % / Redundancy: 5.636 % / CC1/2: 0.988 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.113 / Net I/σ(I): 3.94
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.53-1.621.73420100.1692.431
1.62-1.730.9526350.3711.3251
1.73-1.870.5433010.620.7371
1.87-2.050.2733050.8560.3661
2.05-2.290.14828280.9380.2021
2.29-2.640.08925820.9760.1221
2.64-3.230.06321220.9870.0851
3.23-4.560.05514210.9830.0751
4.56-45.20.0578150.9840.0751

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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: 1.53→45.2 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2045 2553 5 %
Rwork0.1867 --
obs0.1876 51065 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 31 172 2821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092728
X-RAY DIFFRACTIONf_angle_d0.9993703
X-RAY DIFFRACTIONf_dihedral_angle_d6.478371
X-RAY DIFFRACTIONf_chiral_restr0.062384
X-RAY DIFFRACTIONf_plane_restr0.008467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.560.43441360.41272598X-RAY DIFFRACTION94
1.56-1.590.38381380.36042638X-RAY DIFFRACTION99
1.59-1.620.36381410.35182681X-RAY DIFFRACTION100
1.62-1.660.30491420.30422686X-RAY DIFFRACTION100
1.66-1.70.27571410.26792685X-RAY DIFFRACTION100
1.7-1.750.29121420.25672703X-RAY DIFFRACTION100
1.75-1.80.25561420.23642699X-RAY DIFFRACTION100
1.8-1.860.23681430.22312705X-RAY DIFFRACTION100
1.86-1.920.23641410.21822686X-RAY DIFFRACTION100
1.92-20.2261410.18342687X-RAY DIFFRACTION100
2-2.090.2021440.17322719X-RAY DIFFRACTION100
2.09-2.20.16071420.16372694X-RAY DIFFRACTION100
2.2-2.340.2231430.17852717X-RAY DIFFRACTION100
2.34-2.520.1941420.17372701X-RAY DIFFRACTION100
2.52-2.780.22541430.17842707X-RAY DIFFRACTION100
2.78-3.180.22711420.18132715X-RAY DIFFRACTION100
3.18-40.16341430.15432709X-RAY DIFFRACTION99
4-45.20.14611470.14742782X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.5512 Å / Origin y: -0.5893 Å / Origin z: 21.5241 Å
111213212223313233
T0.1558 Å2-0.009 Å2-0.0169 Å2-0.1305 Å2-0.0003 Å2--0.1655 Å2
L0.648 °20.1817 °20.054 °2-1.437 °20.0019 °2--2.0308 °2
S0.0362 Å °-0.0059 Å °0.006 Å °0.29 Å °-0.0246 Å °-0.1121 Å °0.025 Å °0.1002 Å °-0.0115 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 403)

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