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- PDB-4d4b: The catalytic domain, BcGH76, of Bacillus circulans Aman6 in comp... -

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Basic information

Entry
Database: PDB / ID: 4d4b
TitleThe catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with MSMSMe
ComponentsALPHA-1,6-MANNANASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / GH76 / CAZY / MANNAN / ENZYME-CARBOHYDRATE INTERACTION / GLYCOSIDASE INHIBITION / QUANTUM MECHANICS / TRANSITION STATE
Function / homology
Function and homology information


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
Biological speciesBACILLUS CIRCULANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 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)82,7636
Polymers81,8622
Non-polymers9014
Water18,6461035
1
A: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3813
Polymers40,9311
Non-polymers4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3813
Polymers40,9311
Non-polymers4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.550, 85.226, 102.003
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 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 35-375 / 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: Polysaccharide alpha-D-mannopyranose-(1-6)-methyl 1,6-dithio-alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 388.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*SC][a1122h-1a_1-5]/1-2/a6-b1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+S)][a-D-Manp1SH6SH]{[(6+S)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1035 / 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: 2.21 Å3/Da / Density % sol: 44.5 % / 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: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.3→43.8 Å / Num. obs: 178799 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 12.8 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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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: 1.3→65.4 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.341 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15161 8695 4.9 %RANDOM
Rwork0.12097 ---
obs0.12247 170002 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.501 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.3→65.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5382 0 56 1035 6473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195722
X-RAY DIFFRACTIONr_bond_other_d0.0010.025010
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9027817
X-RAY DIFFRACTIONr_angle_other_deg0.86311518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6795712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60125.197304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54815852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6461513
X-RAY DIFFRACTIONr_chiral_restr0.0880.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026703
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021452
X-RAY DIFFRACTIONr_nbd_refined0.2690.22572
X-RAY DIFFRACTIONr_nbd_other0.1840.24953
X-RAY DIFFRACTIONr_nbtor_refined0.190.22907
X-RAY DIFFRACTIONr_nbtor_other0.0810.22280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2153
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1180.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.2113
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3210.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0481.9432747
X-RAY DIFFRACTIONr_mcbond_other2.0481.9432747
X-RAY DIFFRACTIONr_mcangle_it2.4622.9193436
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7612.162975
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1423.1564361
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.535310732
X-RAY DIFFRACTIONr_sphericity_free36.3485254
X-RAY DIFFRACTIONr_sphericity_bonded12.137511329
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 649 -
Rwork0.242 12450 -
obs--99.97 %

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