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- PDB-5m7i: Crystal structure of GH125 1,6-alpha-mannosidase mutant from Clos... -

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Basic information

Entry
Database: PDB / ID: 5m7i
TitleCrystal structure of GH125 1,6-alpha-mannosidase mutant from Clostridium perfringens in complex with 1,6-alpha-mannobiose
Componentsexo-alpha-1,6-mannosidase
KeywordsHYDROLASE / Mannosidase / Carbohydrate chemistry
Function / homology
Function and homology information


carbohydrate metabolic process / metal ion binding
Similarity search - Function
Metal-independent alpha-mannosidase / Metal-independent alpha-mannosidase (GH125) / DUF1237 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Glycoside hydrolase family 125 protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsMales, A. / Alonso-Gil, S. / Fernandes, P. / Williams, S.J. / Rovira, C. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Computational Design of Experiment Unveils the Conformational Reaction Coordinate of GH125 alpha-Mannosidases.
Authors: Alonso-Gil, S. / Males, A. / Fernandes, P.Z. / Williams, S.J. / Davies, G.J. / Rovira, C.
History
DepositionOct 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: exo-alpha-1,6-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2032
Polymers50,8611
Non-polymers3421
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint12 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.296, 43.734, 85.407
Angle α, β, γ (deg.)90.00, 96.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein exo-alpha-1,6-mannosidase


Mass: 50861.008 Da / Num. of mol.: 1 / Mutation: D220N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain 13 / Type A) (bacteria)
Gene: CPE0426 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8XNB2
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 mM MgCl2, 100 mM HEPES pH7.0, 27% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→60.86 Å / Num. obs: 24135 / % possible obs: 91.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.55 / % possible all: 57.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
xia2data reduction
Aimlessdata scaling
RefinementResolution: 2.1→60.86 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.891 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24698 1226 5.1 %RANDOM
Rwork0.19181 ---
obs0.19452 22849 90.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.622 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å2-0 Å2-0.29 Å2
2---2.22 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: 1 / Resolution: 2.1→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 23 125 3626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193594
X-RAY DIFFRACTIONr_bond_other_d0.0020.023259
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.9454870
X-RAY DIFFRACTIONr_angle_other_deg0.92937533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88324.839186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50415609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8311514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024055
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02851
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_it1.1642.7131699
X-RAY DIFFRACTIONr_mcbond_other1.1632.7111698
X-RAY DIFFRACTIONr_mcangle_it1.8474.0632122
X-RAY DIFFRACTIONr_mcangle_other1.8474.0652123
X-RAY DIFFRACTIONr_scbond_it1.3562.8281895
X-RAY DIFFRACTIONr_scbond_other1.3562.8281895
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2184.182749
X-RAY DIFFRACTIONr_long_range_B_refined3.22931.3224164
X-RAY DIFFRACTIONr_long_range_B_other3.22931.3214164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.105→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 60 -
Rwork0.292 1058 -
obs--57.78 %

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