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- PDB-4d4d: The catalytic domain, BcGH76, of Bacillus circulans Aman6 in comp... -

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Basic information

Entry
Database: PDB / ID: 4d4d
TitleThe catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with 1,6-ManIFG
ComponentsALPHA-1,6-MANNANASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / GH76 / CAZY / MANNAN / ENZYME-CARBOHYDRATE INTERACTION / GLYCOSIDASE INHIBITION / TRANSITION STATE
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 ...: / 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
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / alpha-D-mannopyranose / Alpha-1,6-mannanase
Similarity search - Component
Biological speciesBACILLUS CIRCULANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsThompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Stepper, J. / Gilbert, H.J. / Rovira, C. ...Thompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Stepper, J. / Gilbert, H.J. / Rovira, C. / Williams, S.J. / Davies, G.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Evidence for a Boat Conformation at the Transition State of Gh76 Alpha-1,6-Mannanases- Key Enzymes in Bacterial and Fungal Mannoprotein Metabolism
Authors: Thompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Chandler, E. / Temple, M.J. / Stepper, J. / Gilbert, H.J. / Rovira, C. / ...Authors: Thompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Chandler, E. / Temple, M.J. / Stepper, J. / Gilbert, H.J. / Rovira, C. / Williams, S.J. / Davies, G.J.
History
DepositionOct 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Non-polymer description
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 1, 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
Item: _chem_comp.pdbx_synonyms / _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: ALPHA-1,6-MANNANASE
B: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5787
Polymers81,8622
Non-polymers7175
Water16,916939
1
A: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2583
Polymers40,9311
Non-polymers3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3204
Polymers40,9311
Non-polymers3893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.940, 85.841, 103.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALPHA-1,6-MANNANASE


Mass: 40930.859 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CIRCULANS (bacteria) / Strain: TN31 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER
References: UniProt: Q9Z4P9, mannan endo-1,6-alpha-mannosidase
#2: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL


Mass: 147.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO3
#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.: 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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / 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: 45.8 % / Description: NONE
Crystal growpH: 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: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.4→44.2 Å / Num. obs: 146171 / % possible obs: 99.5 % / Observed criterion σ(I): -3.7 / Redundancy: 8.2 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.6 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED NATIVE APO STRUCTURE

Resolution: 1.4→66.01 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.63 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14188 7132 4.9 %RANDOM
Rwork0.11286 ---
obs0.11427 138951 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.069 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.4→66.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5400 0 46 939 6385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195729
X-RAY DIFFRACTIONr_bond_other_d0.0010.025036
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9017820
X-RAY DIFFRACTIONr_angle_other_deg0.863311580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.275711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71125.21309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63715865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6471514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026720
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021460
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_it1.5521.5092740
X-RAY DIFFRACTIONr_mcbond_other1.5521.5082741
X-RAY DIFFRACTIONr_mcangle_it1.8752.2653428
X-RAY DIFFRACTIONr_mcangle_other1.8752.2653429
X-RAY DIFFRACTIONr_scbond_it2.4791.7332989
X-RAY DIFFRACTIONr_scbond_other2.4731.7332989
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8782.5144373
X-RAY DIFFRACTIONr_long_range_B_refined5.00115.2237919
X-RAY DIFFRACTIONr_long_range_B_other3.8213.7057324
X-RAY DIFFRACTIONr_rigid_bond_restr2.123310765
X-RAY DIFFRACTIONr_sphericity_free44.725246
X-RAY DIFFRACTIONr_sphericity_bonded11.471511280
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 519 -
Rwork0.193 10036 -
obs--98.44 %

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