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- PDB-5n0f: The catalytic domain, BcGH76, of Bacillus circulans Aman6 in comp... -

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Basic information

Entry
Database: PDB / ID: 5n0f
TitleThe catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with 1,6-ManSIFG
ComponentsAlpha-1,6-mannanase
KeywordsHYDROLASE / glycoside HYDROLASE / complex / mannanase / S-linked polysaccharide
Function / homology
Function and homology information


catalytic activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase ...Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Galactose-binding-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Chem-7K2 / Alpha-1,6-mannanase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsJin, Y. / Williams, S. / Davies, G.
Funding support United Kingdom, Australia, 2items
OrganizationGrant numberCountry
European Research CouncilAdG322942 United Kingdom
Australian Research CouncilFT130100103 Australia
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: An atypical interaction explains the high-affinity of a non-hydrolyzable S-linked 1,6-alpha-mannanase inhibitor.
Authors: Belz, T. / Jin, Y. / Coines, J. / Rovira, C. / Davies, G.J. / Williams, S.J.
History
DepositionFeb 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_audit_support / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 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: Alpha-1,6-mannanase
B: Alpha-1,6-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5124
Polymers81,8622
Non-polymers6512
Water10,070559
1
A: Alpha-1,6-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2562
Polymers40,9311
Non-polymers3251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1,6-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2562
Polymers40,9311
Non-polymers3251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.050, 86.400, 103.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 39 - 373 / Label seq-ID: 26 - 360

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Alpha-1,6-mannanase


Mass: 40930.859 Da / Num. of mol.: 2 / Mutation: R341Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: aman6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Z4P9
#2: Sugar ChemComp-7K2 / [(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-alpha-D-mannopyranoside / (2~{R},3~{S},4~{S},5~{S},6~{R})-2-[[(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methylsulfanyl]-6-(hydroxymethy l)oxane-3,4,5-triol / isofagomine-thiol-alpha-D-mannopyranoside / [(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-alpha-D-mannoside / [(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-D-mannoside / [(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-mannoside


Type: D-saccharide / Mass: 325.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H23NO7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M AMMONIUM NITRATE, PH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.69→52.32 Å / Num. obs: 84827 / % possible obs: 98.6 % / Redundancy: 7.6 % / Net I/σ(I): 13.4
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6332 / CC1/2: 0.724 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D4D

4d4d


Resolution: 1.69→52.32 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.011 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21794 4223 5 %RANDOM
Rwork0.15222 ---
obs0.15553 80510 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.361 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å2-0 Å20 Å2
2---1.64 Å2-0 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.69→52.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 42 559 6013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195677
X-RAY DIFFRACTIONr_bond_other_d0.0010.024772
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9017737
X-RAY DIFFRACTIONr_angle_other_deg1.025311112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4045686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71125.177311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43315858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8011515
X-RAY DIFFRACTIONr_chiral_restr0.0970.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026478
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021241
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_it3.1442.4522711
X-RAY DIFFRACTIONr_mcbond_other3.1432.4522712
X-RAY DIFFRACTIONr_mcangle_it3.7613.6843387
X-RAY DIFFRACTIONr_mcangle_other3.7613.6843388
X-RAY DIFFRACTIONr_scbond_it4.0572.7472966
X-RAY DIFFRACTIONr_scbond_other4.0572.7472967
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6714.0074344
X-RAY DIFFRACTIONr_long_range_B_refined5.00329.2276629
X-RAY DIFFRACTIONr_long_range_B_other5.00229.2286630
X-RAY DIFFRACTIONr_rigid_bond_restr2.457310449
X-RAY DIFFRACTIONr_sphericity_free31.4515402
X-RAY DIFFRACTIONr_sphericity_bonded14.173510433
Refine LS restraints NCS

Ens-ID: 1 / Number: 22828 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 328 -
Rwork0.193 5995 -
obs--99.83 %

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