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

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Basic information

Entry
Database: PDB / ID: 12nr
TitleCrystal structure of a GH26 enzyme (EiGH26a) in complex with mannose
ComponentsGlycoside hydrolase family 26
KeywordsHYDROLASE / metagenome / manatee / gut microbiota / heteromannan
Function / homologybeta-D-mannopyranose / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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
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)39,9196
Polymers39,3061
Non-polymers6135
Water5,657314
1
A: Glycoside hydrolase family 26
hetero molecules

A: Glycoside hydrolase family 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,83812
Polymers78,6132
Non-polymers1,22610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3950 Å2
ΔGint-1 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.895, 65.310, 83.667
Angle α, β, γ (deg.)90.00, 110.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-772-

HOH

21A-799-

HOH

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Components

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Protein / Sugars , 2 types, 3 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)
#2: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 317 molecules

#3: 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
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M CaCl2, 0.1 M HEPES pH 7.5, 28 % w/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.12→45.22 Å / Num. obs: 820206 / % possible obs: 56 % / Redundancy: 6.343 % / CC1/2: 0.997 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.059 / Net I/σ(I): 4.48
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.12-1.191.071119120.341.5151
1.19-1.270.609115580.5610.8611
1.27-1.370.35106150.7780.4951
1.37-1.50.196102750.9180.2761
1.5-1.680.10685520.9710.1491
1.68-1.940.06574960.9860.091
1.94-2.370.04661540.990.0641
2.37-3.350.03739300.9910.0511
3.35-100.02822040.9950.0371

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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: 1.12→45.22 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1929 6777 5 %
Rwork0.1775 --
obs0.1782 135547 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.12→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 40 314 2973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072770
X-RAY DIFFRACTIONf_angle_d0.9393769
X-RAY DIFFRACTIONf_dihedral_angle_d12.1681005
X-RAY DIFFRACTIONf_chiral_restr0.082393
X-RAY DIFFRACTIONf_plane_restr0.008478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.140.39222290.38424364X-RAY DIFFRACTION100
1.14-1.150.37442210.34874241X-RAY DIFFRACTION100
1.15-1.170.31612310.32834385X-RAY DIFFRACTION100
1.17-1.180.3352250.30834267X-RAY DIFFRACTION100
1.18-1.20.29112280.30044331X-RAY DIFFRACTION100
1.2-1.220.28412270.28414321X-RAY DIFFRACTION100
1.22-1.240.30722260.2754285X-RAY DIFFRACTION100
1.24-1.260.27252280.26414337X-RAY DIFFRACTION100
1.26-1.280.29382250.25794281X-RAY DIFFRACTION100
1.28-1.30.24512300.24264365X-RAY DIFFRACTION100
1.3-1.330.26072270.22794299X-RAY DIFFRACTION100
1.33-1.360.21492250.21714275X-RAY DIFFRACTION100
1.36-1.390.20892280.20044338X-RAY DIFFRACTION100
1.39-1.420.21952300.18794368X-RAY DIFFRACTION100
1.42-1.450.19952250.18224281X-RAY DIFFRACTION100
1.45-1.490.17892280.1724318X-RAY DIFFRACTION100
1.49-1.540.18112260.16034298X-RAY DIFFRACTION100
1.54-1.590.16062270.15424320X-RAY DIFFRACTION100
1.59-1.640.17162280.15214315X-RAY DIFFRACTION100
1.64-1.710.17862290.15184364X-RAY DIFFRACTION100
1.71-1.790.1732280.15624330X-RAY DIFFRACTION100
1.79-1.880.16212290.14944342X-RAY DIFFRACTION100
1.88-20.16272270.15434323X-RAY DIFFRACTION100
2-2.150.15922290.15014345X-RAY DIFFRACTION100
2.15-2.370.17322290.15814341X-RAY DIFFRACTION100
2.37-2.710.18132290.16554358X-RAY DIFFRACTION100
2.71-3.420.18342300.16474362X-RAY DIFFRACTION100
3.42-45.220.16192340.14284446X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.6598 Å / Origin y: -1.1485 Å / Origin z: 21.5058 Å
111213212223313233
T0.1531 Å2-0.001 Å2-0.0278 Å2-0.0861 Å2-0.0005 Å2--0.0918 Å2
L0.4525 °20.1036 °20.0228 °2-0.5272 °20.0041 °2--1.3767 °2
S0.014 Å °-0.0051 Å °0.0071 Å °0.0783 Å °-0.0179 Å °-0.0143 Å °0.01 Å °0.0345 Å °0.0048 Å °
Refinement TLS groupSelection details: all

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