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- PDB-5n6u: Crystal structure of Beta-D-Mannosidase from Dictyoglomus thermop... -

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Basic information

Entry
Database: PDB / ID: 5n6u
TitleCrystal structure of Beta-D-Mannosidase from Dictyoglomus thermophilum.
ComponentsBeta-mannosidase
KeywordsHYDROLASE / mannosidase / thermostable
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / 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, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain ...Mannosidase Ig/CBM-like domain / Beta-mannosidase, Ig-fold domain / Ig-fold domain / Mannosidase Ig/CBM-like domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / Beta-mannosidase
Similarity search - Component
Biological speciesDictyoglomus thermophilum H-6-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsRichet, N. / Lafite, P.
Funding support France, 1items
OrganizationGrant numberCountry
GLYCOPEPSAPR-518N France
CitationJournal: Biochimie / Year: 2017
Title: Is the acid/base catalytic residue mutation in beta-d-mannosidase DtMan from Dictyoglomus thermophilum sufficient enough to provide thioglycoligase activity?
Authors: Guillotin, L. / Richet, N. / Lafite, P. / Daniellou, R.
History
DepositionFeb 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Beta-mannosidase
D: Beta-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,4878
Polymers394,7664
Non-polymers7214
Water37821
1
A: Beta-mannosidase
B: Beta-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,7434
Polymers197,3832
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint1 kcal/mol
Surface area63360 Å2
MethodPISA
2
C: Beta-mannosidase
D: Beta-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,7434
Polymers197,3832
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint1 kcal/mol
Surface area63380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.250, 75.560, 217.880
Angle α, β, γ (deg.)90.00, 92.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 1 - 811 / Label seq-ID: 24 - 834

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Beta-mannosidase /


Mass: 98691.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyoglomus thermophilum H-6-12 (bacteria)
Gene: DICTH_1692 / Production host: Escherichia coli (E. coli) / References: UniProt: B5YAN4, beta-mannosidase
#2: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 24% PEG400, 0.1 M Na-HEPES pH 7, 200 mM MgCl2 / PH range: 7-8

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.913
11-h,-k,l20.087
ReflectionResolution: 3.08→49.5 Å / Num. obs: 71693 / % possible obs: 98.9 % / Redundancy: 3.74 % / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.11 / Rrim(I) all: 0.216 / Net I/σ(I): 7.3
Reflection shellResolution: 3.08→3.14 Å / Rmerge(I) obs: 1.762 / Rpim(I) all: 1.093 / Rrim(I) all: 2.083

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JE8

2je8


Resolution: 3.08→49.5 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.883 / SU B: 16.623 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25483 3813 5 %RANDOM
Rwork0.20376 ---
obs0.20637 71693 88.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--45.63 Å2-0 Å27.1 Å2
2--68.52 Å20 Å2
3----22.89 Å2
Refinement stepCycle: 1 / Resolution: 3.08→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27200 0 44 21 27265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228028
X-RAY DIFFRACTIONr_bond_other_d0.0060.0226384
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.94637912
X-RAY DIFFRACTIONr_angle_other_deg1.4763.00160784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.08353240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40924.111460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.292154968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.06815168
X-RAY DIFFRACTIONr_chiral_restr0.1130.23860
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02131400
X-RAY DIFFRACTIONr_gen_planes_other0.0050.026832
X-RAY DIFFRACTIONr_mcbond_it6.7278.40112972
X-RAY DIFFRACTIONr_mcbond_other6.7278.40112971
X-RAY DIFFRACTIONr_mcangle_it10.40712.59816208
X-RAY DIFFRACTIONr_mcangle_other10.40712.59816209
X-RAY DIFFRACTIONr_scbond_it6.4538.84215056
X-RAY DIFFRACTIONr_scbond_other6.4538.84215057
X-RAY DIFFRACTIONr_scangle_other10.12613.04521705
X-RAY DIFFRACTIONr_long_range_B_refined14.36866.50432256
X-RAY DIFFRACTIONr_long_range_B_other14.36866.50532257
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A1050660.08
12B1050660.08
21A1051080.08
22C1051080.08
31A1037140.09
32D1037140.09
41B1036080.09
42C1036080.09
51B1045840.09
52D1045840.09
61C1036120.1
62D1036120.1
LS refinement shellResolution: 3.08→3.146 Å

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