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- PDB-6far: Structure of the GH99 endo-alpha-mannanase from Bacteroides xylan... -

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Basic information

Entry
Database: PDB / ID: 6far
TitleStructure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-mannoimidazole
ComponentsGlycosyl hydrolase family 71
KeywordsHYDROLASE / complex / GH99
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / membrane
Similarity search - Function
Glycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Chem-MVL / Glycosyl hydrolase family 71
Similarity search - Component
Biological speciesBacteroides xylanisolvens XB1A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFernandes, P.Z. / Petricevic, M. / Sobala, L.F. / Davies, G.J. / Williams, S.J.
Funding support United Kingdom, Australia, 3items
OrganizationGrant numberCountry
European Research Council322942 United Kingdom
Australian Research CouncilFT130100103 Australia
Australian Research CouncilDP120101396 Australia
CitationJournal: Chemistry / Year: 2018
Title: Exploration of Strategies for Mechanism-Based Inhibitor Design for Family GH99 endo-alpha-1,2-Mannanases.
Authors: Fernandes, P.Z. / Petricevic, M. / Sobala, L. / Davies, G.J. / Williams, S.J.
History
DepositionDec 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jul 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 1.3Feb 3, 2021Group: Data collection / Database references / Structure summary
Category: chem_comp / diffrn_source / pdbx_related_exp_data_set
Item: _chem_comp.pdbx_synonyms / _diffrn_source.pdbx_wavelength_list
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase family 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3143
Polymers43,9341
Non-polymers3802
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint4 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.619, 108.619, 67.766
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-776-

HOH

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Components

#1: Protein Glycosyl hydrolase family 71 / Glycosyl hydrolase family 99


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: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / 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
#3: Chemical ChemComp-MVL / (5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL / Mannoimidazole


Mass: 200.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 45.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 3 M sodium acetate, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→76.81 Å / Num. obs: 96147 / % possible obs: 99.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 15.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.02 / Rrim(I) all: 0.057 / Net I/σ(I): 14
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.224 / Num. unique obs: 4400 / CC1/2: 0.486 / Rpim(I) all: 0.754 / Rrim(I) all: 1.376 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
DIALS1.6.3-g2108d754-releasedata reduction
Aimless0.5.32data scaling
REFMAC5.8.0158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M17

5m17


Resolution: 1.3→76.81 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.758 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.043 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16168 4810 5 %RANDOM
Rwork0.13398 ---
obs0.13537 91334 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.958 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.04 Å2
Refinement stepCycle: 1 / Resolution: 1.3→76.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 25 425 3250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023327
X-RAY DIFFRACTIONr_bond_other_d0.0020.022950
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9514618
X-RAY DIFFRACTIONr_angle_other_deg1.00836927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3223.455165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06115542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1811521
X-RAY DIFFRACTIONr_chiral_restr0.0980.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213829
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02758
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_it1.5411.9131535
X-RAY DIFFRACTIONr_mcbond_other1.4921.9111534
X-RAY DIFFRACTIONr_mcangle_it1.8442.8821948
X-RAY DIFFRACTIONr_mcangle_other1.8442.8831949
X-RAY DIFFRACTIONr_scbond_it2.0082.091792
X-RAY DIFFRACTIONr_scbond_other2.0032.091792
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3533.0652621
X-RAY DIFFRACTIONr_long_range_B_refined3.44423.6224056
X-RAY DIFFRACTIONr_long_range_B_other2.97222.7093952
X-RAY DIFFRACTIONr_rigid_bond_restr1.91136277
X-RAY DIFFRACTIONr_sphericity_free25.5625267
X-RAY DIFFRACTIONr_sphericity_bonded9.51556281
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 345 -
Rwork0.279 6321 -
obs--93.4 %

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