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- PDB-12nu: Crystal structure of a GH26 enzyme (EiGH26a) in complex with Mann... -

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Entry
Database: PDB / ID: 12nu
TitleCrystal structure of a GH26 enzyme (EiGH26a) in complex with Mannose-beta-1,4-Glucose-beta-1,4-Mannose
ComponentsGlycoside hydrolase family 26
KeywordsHYDROLASE / metagenome / manatee / gut microbiota / heteromannan
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 Mannose-beta-1,4-Glucose-beta-1,4-Mannose
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

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Assembly

Deposited unit
A: Glycoside hydrolase family 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0823
Polymers39,5551
Non-polymers5272
Water2,324129
1
A: Glycoside hydrolase family 26
hetero molecules

A: Glycoside hydrolase family 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1646
Polymers79,1092
Non-polymers1,0554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)64.850, 65.320, 83.270
Angle α, β, γ (deg.)90.00, 109.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

21A-628-

HOH

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Components

#1: Protein Glycoside hydrolase family 26


Mass: 39554.637 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)
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1b_1-5][a2122h-1b_1-5]/1-2-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Manp]{}}}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.: 129 / 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: 2.11 Å3/Da / Density % sol: 41.57 %
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: Oct 24, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.6→44.67 Å / Num. obs: 43399 / % possible obs: 99.7 % / Redundancy: 6.48 % / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.05 / Net I/σ(I): 6.56
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.6-1.70.238630.9040.2811
1.7-1.810.14838810.9480.2071
1.81-1.960.09338720.9790.131
1.96-2.150.06634730.9880.0921
2.15-2.40.06329010.9870.0871
2.4-2.770.06223380.990.0861
2.77-3.390.0417980.9950.0551
3.39-4.780.02115490.9980.0281
4.78-44.7020.0257920.9980.0341

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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: 1.6→44.67 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2816 2163 5 %
Rwork0.2548 --
obs0.2562 43236 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 35 129 2764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052715
X-RAY DIFFRACTIONf_angle_d0.8163690
X-RAY DIFFRACTIONf_dihedral_angle_d12.821975
X-RAY DIFFRACTIONf_chiral_restr0.052391
X-RAY DIFFRACTIONf_plane_restr0.006464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.38581420.35242698X-RAY DIFFRACTION98
1.64-1.680.33861430.33042710X-RAY DIFFRACTION100
1.68-1.720.35931430.32582720X-RAY DIFFRACTION100
1.72-1.770.31591450.31412752X-RAY DIFFRACTION100
1.77-1.830.36931430.3122724X-RAY DIFFRACTION100
1.83-1.90.31991440.31242736X-RAY DIFFRACTION100
1.9-1.970.35251440.29162720X-RAY DIFFRACTION100
1.97-2.060.32261430.29352723X-RAY DIFFRACTION100
2.06-2.170.3161450.27982754X-RAY DIFFRACTION100
2.17-2.310.31591450.28492753X-RAY DIFFRACTION100
2.31-2.490.30811430.28672712X-RAY DIFFRACTION100
2.49-2.740.33111450.27382752X-RAY DIFFRACTION100
2.74-3.130.25221440.2462753X-RAY DIFFRACTION100
3.13-3.940.24041450.20812749X-RAY DIFFRACTION100
3.95-44.670.19771490.18262817X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.7047 Å / Origin y: -0.9862 Å / Origin z: 21.4381 Å
111213212223313233
T0.1957 Å20.0025 Å2-0.096 Å2-0.0745 Å20 Å2--0.1642 Å2
L0.7083 °20.1595 °2-0.3839 °2-0.6502 °2-0.1324 °2--1.957 °2
S0.0033 Å °0.0325 Å °0.0057 Å °0.0853 Å °-0.0078 Å °-0.0374 Å °0.002 Å °0.1099 Å °0.0137 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 321)

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