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- PDB-29qd: CjMan26C bound to covalent beta-mannanase inhibitor -

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Basic information

Entry
Database: PDB / ID: 29qd
TitleCjMan26C bound to covalent beta-mannanase inhibitor
ComponentsEndo-1, 4-beta mannanase, putative, man26C
KeywordsHYDROLASE / Beta-Mannan / GH26 / endo-mannanase / cyclophellitol / covalent
Function / homology
Function and homology information


substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity
Similarity search - Function
Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-D-mannopyranose / Chem-YLL / Endo-1, 4-beta mannanase, putative, man26C
Similarity search - Component
Biological speciesCellvibrio japonicus Ueda107 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsMcGregor, N.G.S. / Davies, G.J.
Funding supportEuropean Union, United Kingdom, Spain, 5items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2020-SyG-951231European Union
Royal SocietyKen Murray Research Professorship United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T017805/1 United Kingdom
Spanish Ministry of Science, Innovation, and UniversitiesPID2023-147939NB-I00 Spain
CitationJournal: Chem Sci / Year: 2026
Title: The development of activity-based mannanase probes.
Authors: Tedeschi, M. / Lit, V.A.J. / McGregor, N.G.S. / Gote, T. / Kooloth Valappil, P. / Arentshorst, M. / Florea, B.I. / Gagestein, B. / Armstrong, Z. / Codee, J.D.C. / Nin-Hill, A. / Rovira, C. / ...Authors: Tedeschi, M. / Lit, V.A.J. / McGregor, N.G.S. / Gote, T. / Kooloth Valappil, P. / Arentshorst, M. / Florea, B.I. / Gagestein, B. / Armstrong, Z. / Codee, J.D.C. / Nin-Hill, A. / Rovira, C. / Ram, A.F.J. / Davies, G.J. / Overkleeft, H.S.
History
DepositionMar 29, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Endo-1, 4-beta mannanase, putative, man26C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8775
Polymers45,4561
Non-polymers4204
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.802, 84.802, 245.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Endo-1, 4-beta mannanase, putative, man26C


Mass: 45456.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio japonicus Ueda107 (bacteria)
Gene: man26C, CJA_0236 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B3PGI1, mannan endo-1,4-beta-mannosidase
#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.: 1 / 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
#3: Chemical ChemComp-YLL / (1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL


Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2% tacsimate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.16→73.43 Å / Num. obs: 180225 / % possible obs: 100 % / Observed criterion σ(I): 0.5 / Redundancy: 39 % / CC1/2: 0.999 / Net I/σ(I): 11.6
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 6.1 % / Num. unique obs: 8769 / CC1/2: 0.33 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→70.469 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.14 / WRfactor Rwork: 0.124 / SU B: 0.944 / SU ML: 0.018 / Average fsc free: 0.9582 / Average fsc work: 0.9632 / Cross valid method: FREE R-VALUE / ESU R: 0.027 / ESU R Free: 0.027
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1488 8303 5.095 %
Rwork0.1297 154664 -
all0.131 --
obs-162967 99.957 %
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: 12.788 Å2
Baniso -1Baniso -2Baniso -3
1--0.027 Å2-0.014 Å2-0 Å2
2---0.027 Å20 Å2
3---0.088 Å2
Refinement stepCycle: LAST / Resolution: 1.2→70.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 25 412 3374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133222
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172901
X-RAY DIFFRACTIONr_angle_refined_deg1.9731.6434425
X-RAY DIFFRACTIONr_angle_other_deg1.6441.5856696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2865416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79422.308195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08115501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5591522
X-RAY DIFFRACTIONr_chiral_restr0.1250.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02810
X-RAY DIFFRACTIONr_nbd_refined0.2310.2691
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22717
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21555
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.10.21418
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2270
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.24
X-RAY DIFFRACTIONr_nbd_other0.2050.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3210.225
X-RAY DIFFRACTIONr_mcbond_it2.7671.1361522
X-RAY DIFFRACTIONr_mcbond_other2.6321.1331521
X-RAY DIFFRACTIONr_mcangle_it2.3851.7091915
X-RAY DIFFRACTIONr_mcangle_other2.4071.7111916
X-RAY DIFFRACTIONr_scbond_it3.611.3311700
X-RAY DIFFRACTIONr_scbond_other3.6091.3321701
X-RAY DIFFRACTIONr_scangle_it3.4371.9172485
X-RAY DIFFRACTIONr_scangle_other3.4361.9172486
X-RAY DIFFRACTIONr_lrange_it3.42214.4513921
X-RAY DIFFRACTIONr_lrange_other3.19913.7383806
X-RAY DIFFRACTIONr_rigid_bond_restr7.59136123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.2326590.21411195X-RAY DIFFRACTION99.9494
1.231-1.2650.2215860.20510998X-RAY DIFFRACTION99.9827
1.265-1.3020.2075100.1910767X-RAY DIFFRACTION99.9911
1.302-1.3420.1975490.16410398X-RAY DIFFRACTION100
1.342-1.3860.1765500.14810079X-RAY DIFFRACTION99.9906
1.386-1.4340.1645070.1329788X-RAY DIFFRACTION99.9903
1.434-1.4880.1585180.1179428X-RAY DIFFRACTION99.9799
1.488-1.5490.1375060.1029078X-RAY DIFFRACTION100
1.549-1.6180.1244840.0968723X-RAY DIFFRACTION100
1.618-1.6970.124630.0918379X-RAY DIFFRACTION100
1.697-1.7890.1174160.097982X-RAY DIFFRACTION99.9881
1.789-1.8970.1344400.0977524X-RAY DIFFRACTION100
1.897-2.0280.1323790.1077149X-RAY DIFFRACTION99.9867
2.028-2.1910.1453570.1146660X-RAY DIFFRACTION100
2.191-2.40.1263460.1046146X-RAY DIFFRACTION100
2.4-2.6830.1232740.1125652X-RAY DIFFRACTION100
2.683-3.0980.1462690.1334982X-RAY DIFFRACTION99.981
3.098-3.7940.1472090.1444303X-RAY DIFFRACTION100
3.794-5.3650.1331610.1443425X-RAY DIFFRACTION100
5.365-70.4690.2121200.2162011X-RAY DIFFRACTION99.9531

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