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- PDB-5axh: Crystal structure of thermophilic dextranase from Thermoanaerobac... -

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Basic information

Entry
Database: PDB / ID: 5axh
TitleCrystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus, D312G mutant in complex with isomaltohexaose
ComponentsDextranase
KeywordsHYDROLASE / glycoside hydrolase family 66
Function / homology
Function and homology information


dextranase / dextranase activity / metabolic process / membrane
Similarity search - Function
Glycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich ...Glycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Dextranase
Similarity search - Component
Biological speciesThermoanaerobacter pseudethanolicus ATCC 33223 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSuzuki, N. / Kishine, N. / Fujimoto, Z. / Sakurai, M. / Momma, M. / Ko, J.A. / Nam, S.H. / Kimura, A. / Kim, Y.M.
Funding support Japan, Korea, Republic Of, 2items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries25001A Japan
National Research Foundation of Korea2010-0020141 Korea, Republic Of
CitationJournal: J.Biochem. / Year: 2016
Title: Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus
Authors: Suzuki, N. / Kishine, N. / Fujimoto, Z. / Sakurai, M. / Momma, M. / Ko, J.A. / Nam, S.H. / Kimura, A. / Kim, Y.M.
History
DepositionJul 29, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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_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 2.1Nov 8, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dextranase
B: Dextranase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,87610
Polymers142,6552
Non-polymers2,2228
Water10,701594
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint5 kcal/mol
Surface area43200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.334, 99.179, 169.254
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, 2 molecules AB

#1: Protein Dextranase /


Mass: 71327.484 Da / Num. of mol.: 2 / Fragment: UNP residues 3-610 / Mutation: D312G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter pseudethanolicus ATCC 33223 (bacteria)
Strain: ATCC 33223 / Gene: Teth39_0264 / Plasmid: pET23d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B0KBZ7, dextranase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a6-b1_b6-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2-2-2/a6-b1_b6-c1_c6-d1_d6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 600 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.12 M sodium dihydrogenphosphate dihydrate, 1.68 M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→38.92 Å / Num. obs: 67398 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.127 / Rsym value: 0.122 / Net I/σ(I): 22.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 3.6 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AXG

5axg


Resolution: 2.2→38.92 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.739 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20516 3350 5 %RANDOM
Rwork0.1602 ---
obs0.16245 63212 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.667 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.2→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9566 0 144 594 10304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.029990
X-RAY DIFFRACTIONr_bond_other_d0.0020.029249
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.95813550
X-RAY DIFFRACTIONr_angle_other_deg0.888321346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53751173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40625.069507
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.331151689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2941532
X-RAY DIFFRACTIONr_chiral_restr0.0810.21434
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022360
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_it1.8523.2624693
X-RAY DIFFRACTIONr_mcbond_other1.8513.2614692
X-RAY DIFFRACTIONr_mcangle_it2.9254.8855865
X-RAY DIFFRACTIONr_mcangle_other2.9254.8865866
X-RAY DIFFRACTIONr_scbond_it2.3883.6075297
X-RAY DIFFRACTIONr_scbond_other2.3863.6025289
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9055.2777673
X-RAY DIFFRACTIONr_long_range_B_refined5.72526.61911758
X-RAY DIFFRACTIONr_long_range_B_other5.68426.5711675
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 224 -
Rwork0.202 4289 -
obs--91.67 %

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