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- PDB-5lyr: Structure of the GH99 endo-alpha-mannanase from Bacteroides xylan... -

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Basic information

Entry
Database: PDB / ID: 5lyr
TitleStructure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-noeuromycin
ComponentsGlycosyl hydrolase family 71
KeywordsHYDROLASE / endomannanase endomannosidase GH99 noeuromycin hydrolase N-glycosylation glycosylation inhibitor inhibition shape charge
Function / homology
Function and homology information


alpha-mannosidase activity / membrane
Similarity search - Function
Glycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / alpha-D-mannopyranose / Chem-MNM / Glycosyl hydrolase family 71
Similarity search - Component
Biological speciesBacteroides xylanisolvens XB1A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsPetricevic, M. / Sobala, L.F. / Fernandes, P.Z. / Raich, L. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Sollogoub, M. / Rovira, C. ...Petricevic, M. / Sobala, L.F. / Fernandes, P.Z. / Raich, L. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Sollogoub, M. / Rovira, C. / Jimenez-Barbero, J. / Davies, G.J. / Williams, S.J.
Funding support United Kingdom, Australia, Spain, 7items
OrganizationGrant numberCountry
European Research Council322942 United Kingdom
Australian Research CouncilFT130100103 Australia
Australian Research CouncilDP120101396 Australia
Spanish Ministry of Economy and CompetitivenessCTQ2014-55174 Spain
Spanish Ministry of Economy and CompetitivenessCTQ2015-64597-C2-1P Spain
Spanish Ministry of Economy and CompetitivenessCTQ2015-68756-R Spain
Generalitat de Catalunya2014SGR-987 Spain
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-alpha-1,2-Mannanase.
Authors: Petricevic, M. / Sobala, L.F. / Fernandes, P.Z. / Raich, L. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Sollogoub, M. / Jimenez-Barbero, J. / Rovira, C. / Davies, G.J. / Williams, S.J.
History
DepositionSep 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Jul 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 1.4Nov 25, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.5Feb 10, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.6Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase family 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3955
Polymers43,9341
Non-polymers4614
Water7,602422
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint5 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.513, 108.513, 67.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-740-

HOH

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Components

#1: Protein Glycosyl hydrolase family 71


Mass: 43933.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides xylanisolvens XB1A (bacteria)
Gene: BXY_34140 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6D1V7
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-MNM / (2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 3 M sodium acetate, pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.14→76.73 Å / Num. obs: 134771 / % possible obs: 94.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.6
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 1.158 / Mean I/σ(I) obs: 0.7 / CC1/2: 0.387 / % possible all: 61.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
DIALS1.0-0-g66ac5d4data reduction
Aimless0.5.21data scaling
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTF

4utf


Resolution: 1.14→76.73 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.004 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14333 6708 5 %RANDOM
Rwork0.12375 ---
obs0.12473 127995 94.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.123 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.14→76.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 30 422 3266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023422
X-RAY DIFFRACTIONr_bond_other_d0.0020.023122
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9514762
X-RAY DIFFRACTIONr_angle_other_deg1.05737275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8715474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13123.158171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44115561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3511525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214030
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02865
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1651.61579
X-RAY DIFFRACTIONr_mcbond_other1.1411.5971576
X-RAY DIFFRACTIONr_mcangle_it1.5472.4122007
X-RAY DIFFRACTIONr_mcangle_other1.5482.4142008
X-RAY DIFFRACTIONr_scbond_it1.611.7631843
X-RAY DIFFRACTIONr_scbond_other1.6091.7631843
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9732.5812696
X-RAY DIFFRACTIONr_long_range_B_refined3.20219.7864108
X-RAY DIFFRACTIONr_long_range_B_other2.71818.9834018
X-RAY DIFFRACTIONr_rigid_bond_restr1.46336542
X-RAY DIFFRACTIONr_sphericity_free30.3055279
X-RAY DIFFRACTIONr_sphericity_bonded8.37556526
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 335 -
Rwork0.407 6339 -
obs--63.3 %

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