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- PDB-7op7: Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-conf... -

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Basic information

Entry
Database: PDB / ID: 7op7
TitleBacteroides thetaiotaomicron mannosidase GH2 with beta-manno-configured N-alkyl cyclophellitol aziridine
ComponentsBeta-mannosidase
KeywordsHYDROLASE / mannosidase / cyclophellitol aziridine
Function / homology
Function and homology information


beta-mannosidase / beta-mannosidase activity / glycoprotein catabolic process / carbohydrate metabolic process / lysosome / extracellular region
Similarity search - Function
: / Mannosidase Ig/CBM-like domain / Beta-mannosidase, Ig-fold domain / Ig-fold domain / Mannosidase Ig/CBM-like domain / : / Glycosyl hydrolase 2 galactose-binding domain-like / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily ...: / Mannosidase Ig/CBM-like domain / Beta-mannosidase, Ig-fold domain / Ig-fold domain / Mannosidase Ig/CBM-like domain / : / Glycosyl hydrolase 2 galactose-binding domain-like / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
BROMIDE ION / Chem-VEE / Beta-mannosidase B
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMcGregor, N.G.S. / Beenakker, T.J.M. / Kuo, C. / Wong, C. / Offen, W.A. / Armstrong, Z. / Codee, J.D.C. / Aerts, J.M.F.G. / Florea, B.I. / Overkleeft, H.S. / Davies, G.J.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004819/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
European Research Council (ERC)Synergy Grant 951231-CarbocentreEuropean Union
CitationJournal: Org.Biomol.Chem. / Year: 2022
Title: Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases.
Authors: McGregor, N.G.S. / Kuo, C.L. / Beenakker, T.J.M. / Wong, C.S. / Offen, W.A. / Armstrong, Z. / Florea, B.I. / Codee, J.D.C. / Overkleeft, H.S. / Aerts, J.M.F.G. / Davies, G.J.
History
DepositionMay 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)200,65863
Polymers196,5822
Non-polymers4,07661
Water14,916828
1
A: Beta-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,07626
Polymers98,2911
Non-polymers1,78525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,58237
Polymers98,2911
Non-polymers2,29036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.761, 114.707, 98.639
Angle α, β, γ (deg.)90.000, 112.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-mannosidase


Mass: 98291.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: beta-mannosidase without signal peptide sequence and with C-terminal his6 tag
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_0458 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8AAK6

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Non-polymers , 5 types, 889 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-VEE / (1R,2S,3R,4S,5R,6R)-5-(8-azidooctylamino)-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol / N-alkyl mannocyclophellitol aziridine


Mass: 330.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Br
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 828 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 3350, sodium bromide, MES buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 1.85→67.66 Å / Num. obs: 158303 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rpim(I) all: 0.053 / Net I/σ(I): 8.3
Reflection shellResolution: 1.85→1.88 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 7816 / CC1/2: 0.5 / Rpim(I) all: 1.004 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JE8.pdb

2je8


Resolution: 1.85→67.66 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.432 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE ALKYL CHAIN OF THE LIGAND IN MOLECULE A IS MODELLED PARTLY, WITH SOME ATOMS AT PARTIAL OCCUPANCY. THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE ALKYL CHAIN OF THE LIGAND IN MOLECULE A IS MODELLED PARTLY, WITH SOME ATOMS AT PARTIAL OCCUPANCY. THE LIGAND IN MOLECULE B IS MODELLED AT HALF OCCUPANCY, AND AN ETHYLENE GLYCOL AT HALF OCCUPANCY IS ALSO BOUND IN THE ACTIVE SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 7873 5 %RANDOM
Rwork0.1891 ---
obs0.1918 150387 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.07 Å2 / Biso mean: 32.299 Å2 / Biso min: 12.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.52 Å2-0 Å2-0.86 Å2
2---0.19 Å2-0 Å2
3---2.54 Å2
Refinement stepCycle: final / Resolution: 1.85→67.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13533 0 181 828 14542
Biso mean--41.13 34.93 -
Num. residues----1677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01314496
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713238
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.64819711
X-RAY DIFFRACTIONr_angle_other_deg1.4411.57430501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.88951784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81322.444802
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.624152361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6471588
X-RAY DIFFRACTIONr_chiral_restr0.0920.21830
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023536
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 587 -
Rwork0.343 11075 -
all-11662 -
obs--99.73 %

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