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- PDB-5jug: Structure of an inactive (E45Q) variant of a beta-1,4-mannanase, ... -

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Basic information

Entry
Database: PDB / ID: 5jug
TitleStructure of an inactive (E45Q) variant of a beta-1,4-mannanase, SsGH134, in complex with Man5
Componentsbeta-1,4-mannanase
KeywordsHYDROLASE / beta-1 / 4-mannanase / carbohydrate degrading / glycosyl hydrolase
Function / homology: / Glycosyl hydrolase family 134 / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / alpha-D-mannopyranose / Beta-1,4-mannanase
Function and homology information
Biological speciesStreptomyces sp. NRRL B-16215 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsJin, Y. / Petricevic, M. / Goddard-Borger, E.D. / Williams, S.J. / Davies, G.J.
Funding support United Kingdom, Australia, 2items
OrganizationGrant numberCountry
European Research CouncilAdG-322942 United Kingdom
Australian Research Council Australia
CitationJournal: ACS Cent Sci / Year: 2016
Title: A beta-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism.
Authors: Jin, Y. / Petricevic, M. / John, A. / Raich, L. / Jenkins, H. / Portela De Souza, L. / Cuskin, F. / Gilbert, H.J. / Rovira, C. / Goddard-Borger, E.D. / Williams, S.J. / Davies, G.J.
History
DepositionMay 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_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 / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7295
Polymers17,5921
Non-polymers1,1364
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint17 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.707, 53.841, 82.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein beta-1,4-mannanase


Mass: 17592.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Streptomyces sp. NRRL B-24484, Taxonomy ID:1463833
Source: (gene. exp.) Streptomyces sp. NRRL B-16215 (bacteria)
Strain: NRRL B-24484 / Plasmid: pHisMALP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon plus
References: UniProt: A0A1L1QK16*PLUS, mannan endo-1,4-beta-mannosidase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#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.: 1
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 , 3 types, 230 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The protein stock in the buffer of 20 mM sodium phosphate, pH7.2 and 200 mM NaCl is mixed 1:1 with the precipitant consist of 20 % PEG6000, 0.15-0.2 M CaCl2, and 0.1 M NaHEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 0.96→45.11 Å / Num. obs: 84396 / % possible obs: 84.1 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.4
Reflection shellResolution: 0.96→0.98 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.1 / % possible all: 29.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
ACORNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alpha-helical fragment

Resolution: 0.96→45.11 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.61 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.021 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14133 4166 4.9 %RANDOM
Rwork0.12173 ---
obs0.1227 80165 83.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 9.503 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-0 Å2
2---0.12 Å20 Å2
3---0.25 Å2
Refinement stepCycle: 1 / Resolution: 0.96→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 75 228 1539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191390
X-RAY DIFFRACTIONr_bond_other_d0.0020.021234
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.9871905
X-RAY DIFFRACTIONr_angle_other_deg1.00832854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9935183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74624.03262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.38815194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.197159
X-RAY DIFFRACTIONr_chiral_restr0.1080.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021608
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02339
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_it1.0050.779687
X-RAY DIFFRACTIONr_mcbond_other1.0060.779686
X-RAY DIFFRACTIONr_mcangle_it1.3711.178861
X-RAY DIFFRACTIONr_mcangle_other1.3711.178862
X-RAY DIFFRACTIONr_scbond_it1.3520.873703
X-RAY DIFFRACTIONr_scbond_other1.3490.872703
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7621.2711037
X-RAY DIFFRACTIONr_long_range_B_refined2.9698.031856
X-RAY DIFFRACTIONr_long_range_B_other2.9678.0291856
X-RAY DIFFRACTIONr_rigid_bond_restr1.79832624
X-RAY DIFFRACTIONr_sphericity_free26.134548
X-RAY DIFFRACTIONr_sphericity_bonded6.96252767
LS refinement shellResolution: 0.96→0.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 115 -
Rwork0.332 1987 -
obs--28.71 %

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