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- PDB-2whl: Understanding how diverse mannanases recognise heterogeneous subs... -

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Basic information

Entry
Database: PDB / ID: 2whl
TitleUnderstanding how diverse mannanases recognise heterogeneous substrates
ComponentsBETA-MANNANASE
KeywordsHYDROLASE / MANNANASE / GLYCOSIDE HYDROLASE
Function / homology
Function and homology information


beta-mannosidase activity / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / glucan catabolic process / membrane
Similarity search - Function
: / Mannanase, galactose-binding domain-like / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Beta-mannanase
Similarity search - Component
Biological speciesBACILLUS AGARADHAERENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTailford, L.E. / Ducros, V.M.A. / Flint, J.E. / Roberts, S.M. / Morland, C. / Zechel, D.L. / Smith, N. / Bjornvad, M.E. / Borchert, T.V. / Wilson, K.S. ...Tailford, L.E. / Ducros, V.M.A. / Flint, J.E. / Roberts, S.M. / Morland, C. / Zechel, D.L. / Smith, N. / Bjornvad, M.E. / Borchert, T.V. / Wilson, K.S. / Davies, G.J. / Gilbert, H.J.
CitationJournal: Biochemistry / Year: 2009
Title: Understanding How Diverse -Mannanases Recognise Heterogeneous Substrates.
Authors: Tailford, L.E. / Ducros, V.M.A. / Flint, J.E. / Roberts, S.M. / Morland, C. / Zechel, D.L. / Smith, N. / Bjornvad, M.E. / Borchert, T.V. / Wilson, K.S. / Davies, G.J. / Gilbert, H.J.
History
DepositionMay 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _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_alt_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 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3263
Polymers32,7631
Non-polymers5632
Water4,918273
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.255, 63.690, 83.577
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 BETA-MANNANASE / BAMAN5


Mass: 32762.746 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-330 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS AGARADHAERENS (bacteria) / Strain: NCIMB 40482 / Production host: BACILLUS SUBTILIS (bacteria)
References: UniProt: Q5YEX6, mannan endo-1,4-beta-mannosidase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1a_1-5][a1122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 37 TO SER

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.09 % / Description: NONE
Crystal growDetails: 1.6M NA/K PO4, 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 1.4→19.73 Å / Num. obs: 62370 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 27
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.5 / % possible all: 68

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Processing

Software
NameVersionClassification
REFMAC5.4.0062refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WHJ

2whj


Resolution: 1.4→50.64 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.442 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2980 5.1 %RANDOM
Rwork0.15 ---
obs0.152 55790 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.22 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å20 Å20 Å2
2---2.32 Å20 Å2
3----2.2 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 38 273 2623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212474
X-RAY DIFFRACTIONr_bond_other_d0.0020.021575
X-RAY DIFFRACTIONr_angle_refined_deg1.961.9223384
X-RAY DIFFRACTIONr_angle_other_deg1.61833826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17624.923130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3415377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4321513
X-RAY DIFFRACTIONr_chiral_restr0.3040.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02508
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_it2.1671.51483
X-RAY DIFFRACTIONr_mcbond_other1.2611.5620
X-RAY DIFFRACTIONr_mcangle_it2.93922385
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2893991
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7834.5996
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.3634049
X-RAY DIFFRACTIONr_sphericity_free12.1573273
X-RAY DIFFRACTIONr_sphericity_bonded7.54633984
LS refinement shellResolution: 1.4→1.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 146 -
Rwork0.261 2503 -
obs--58.35 %

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