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- PDB-2je8: Structure of a beta-mannosidase from Bacteroides thetaiotaomicron -

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Basic information

Entry
Database: PDB / ID: 2je8
TitleStructure of a beta-mannosidase from Bacteroides thetaiotaomicron
ComponentsBETA-MANNOSIDASE
KeywordsHYDROLASE / BETA-MANNOSIDASE / GLYCOSIDE HYDROLASE
Function / homology
Function and homology information


beta-mannosidase / beta-mannosidase activity / glycoprotein catabolic process / carbohydrate metabolic process / extracellular region
Similarity search - Function
Mannosidase Ig/CBM-like domain / Beta-mannosidase, Ig-fold domain / Ig-fold domain / Mannosidase Ig/CBM-like domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases ...Mannosidase Ig/CBM-like domain / Beta-mannosidase, Ig-fold domain / Ig-fold domain / Mannosidase Ig/CBM-like domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsTailford, L.E. / Money, V.A. / Smith, N.L. / Dumon, C. / Davies, G.J. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Mannose Foraging by Bacteroides Thetaiotaomicron: Structure and Specificity of the Beta-Mannosidase, Btman2A.
Authors: Tailford, L.E. / Money, V.A. / Smith, N.L. / Dumon, C. / Davies, G.J. / Gilbert, H.J.
History
DepositionJan 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-MANNOSIDASE
B: BETA-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,17418
Polymers196,3562
Non-polymers1,81816
Water33,4361856
1
A: BETA-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8438
Polymers98,1781
Non-polymers6657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,33110
Polymers98,1781
Non-polymers1,1539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.463, 115.997, 99.146
Angle α, β, γ (deg.)90.00, 113.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99615, 0.08578, -0.01811), (0.08354, 0.86612, -0.49281), (-0.02659, -0.49243, -0.86995)
Vector: 5.6118, 14.05042, 69.82903)

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Components

#1: Protein BETA-MANNOSIDASE


Mass: 98177.969 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-864
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Description: DIRECTLY FROM ATCC / Plasmid: PLT001 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8AAK6, beta-mannosidase
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1856 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 42.52 %
Crystal growpH: 7
Details: 0.15-0.35 M NABR, 6-12% W/V PEG 3350 AND 0.1 M BIS TRIS PROPANE PH7 OR 0.08-0.2 M KSCN 8-15% W/V PEG 3350 AND 0.1 M BIS TRIS PROPANE, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 26, 2005 / Details: TOROIDAL MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→39.56 Å / Num. obs: 2 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
MLPHAREphasing
REFMAC5.3.0021refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→39.56 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.628 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 10324 5 %RANDOM
Rwork0.155 ---
obs0.157 197589 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.12 Å2
2--0.04 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13693 0 115 1856 15664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02214570
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9519857
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62651805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4123.939726
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.614152490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4261593
X-RAY DIFFRACTIONr_chiral_restr0.1610.22106
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211261
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.27132
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.29878
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.21617
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.290
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4341.58838
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.564214006
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.67136662
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0564.55788
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 788
Rwork0.201 14500

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