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- PDB-6zbx: Structure of the catalytic domain of the Bacillus circulans alpha... -

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Basic information

Entry
Database: PDB / ID: 6zbx
TitleStructure of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6- alpha-manno-cyclophellitol carbasugar-stabilised trisaccharide inhibitor
Components
  • Alpha-1,6-mannanase
  • UNK-UNK-UNK-UNK
KeywordsHYDROLASE / mannanase / cyclophellitol / epoxide
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 / Six-hairpin glycosidase superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Chem-M96 / alpha-D-mannopyranose / Chem-PBW / Alpha-1,6-mannanase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSchroeder, S. / Offen, W.A. / Jin, Y. / De Boer, C. / Enoterpi, J. / Marino, L. / van der Marel, G.A. / Codee, J.D.C. / Overkleeft, H.S. / Davies, G.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004819/1 United Kingdom
CitationJournal: Chemistry / Year: 2021
Title: Development of Non-Hydrolysable Oligosaccharide Activity-Based Inactivators for Endoglycanases: A Case Study on alpha-1,6 Mannanases.
Authors: Schroder, S.P. / Offen, W.A. / Males, A. / Jin, Y. / de Boer, C. / Enotarpi, J. / Marino, L. / van der Marel, G.A. / Florea, B.I. / Codee, J.D.C. / Overkleeft, H.S. / Davies, G.J.
History
DepositionJun 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.3Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 24, 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
Revision 1.5Oct 9, 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: Alpha-1,6-mannanase
B: Alpha-1,6-mannanase
E: UNK-UNK-UNK-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,44911
Polymers82,2203
Non-polymers1,2298
Water10,503583
1
A: Alpha-1,6-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5455
Polymers40,9311
Non-polymers6154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint6 kcal/mol
Surface area13130 Å2
MethodPISA
2
B: Alpha-1,6-mannanase
E: UNK-UNK-UNK-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9046
Polymers41,2892
Non-polymers6154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint3 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.373, 51.087, 66.198
Angle α, β, γ (deg.)93.610, 92.360, 98.210
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide / Sugars , 3 types, 5 molecules ABE

#1: Protein Alpha-1,6-mannanase


Mass: 40930.859 Da / Num. of mol.: 2 / Mutation: R341Q
Source method: isolated from a genetically manipulated source
Details: N-terminally His-tagged catalytic domain of BcGH76 with mutation R341Q
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: aman6 / Production host: Escherichia coli (E. coli) / Variant (production host): Tuner (DE3) / References: UniProt: Q9Z4P9
#2: Protein/peptide UNK-UNK-UNK-UNK


Mass: 358.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Peptide, probably connected to either chain A or B, but unable to be identified
Source: (gene. exp.) Bacillus circulans (bacteria) / Production host: Escherichia coli (E. coli)
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 589 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PBW / (1~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol


Mass: 194.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O6
#5: Chemical ChemComp-M96 / (1~{S},2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol


Mass: 178.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 1.92 Å3/Da / Density % sol: 36.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→50.49 Å / Num. obs: 127986 / % possible obs: 95.1 % / Redundancy: 3.5 % / CC1/2: 0.977 / Rpim(I) all: 0.026 / Net I/σ(I): 14.1
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3 % / Num. unique obs: 5907 / CC1/2: 0.638 / Rpim(I) all: 0.398 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D4A.PDB

4d4a


Resolution: 1.35→50.49 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.458 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THERE ARE REGIONS OF UNMODELLED DENSITY NEAR THE SIDE CHAINS OF PHE122A, ASN206A AND 206B, ASP266A AND TYR319A. THERE IS A PEPTIDE CHAIN OF 4 AMINO ACIDS WHICH COULD NOT BE ASSIGNED WITH ...Details: THERE ARE REGIONS OF UNMODELLED DENSITY NEAR THE SIDE CHAINS OF PHE122A, ASN206A AND 206B, ASP266A AND TYR319A. THERE IS A PEPTIDE CHAIN OF 4 AMINO ACIDS WHICH COULD NOT BE ASSIGNED WITH CONFIDENCE TO EITHER CHAIN A OR B AND HAVE THEREFORE BEEN MODELLED AS UNK RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 6308 4.9 %RANDOM
Rwork0.1333 ---
obs0.1355 121581 95.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.97 Å2 / Biso mean: 16.658 Å2 / Biso min: 7.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20.35 Å2-0.26 Å2
2---0.04 Å2-0.12 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 1.35→50.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5368 0 76 584 6028
Biso mean--19.57 29.65 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135702
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174781
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.6497782
X-RAY DIFFRACTIONr_angle_other_deg1.7261.59911114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2465695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3524.423312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65115833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7541515
X-RAY DIFFRACTIONr_chiral_restr0.1110.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026557
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021256
X-RAY DIFFRACTIONr_rigid_bond_restr3.479310479
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 496 -
Rwork0.217 8382 -
all-8878 -
obs--89.37 %

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