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

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Basic information

Entry
Database: PDB / ID: 5axg
TitleCrystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus
ComponentsDextranase
KeywordsHYDROLASE / glycoside hydrolase family 66
Function / homology
Function and homology information


dextranase / dextranase activity / 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: 1.85 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: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_symmetry

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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)144,35021
Polymers142,7712
Non-polymers1,57919
Water16,015889
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-23 kcal/mol
Surface area43750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.342, 98.992, 171.130
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: 71385.523 Da / Num. of mol.: 2 / Fragment: UNP residues 3-610
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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Non-polymers , 5 types, 908 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / 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: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 1.35 M sodium dihydrogenphosphate dihydrate, 0.9 M potassium phosphate dibasic, 0.2 M lithium sulfate, 0.1 M 3-(cyclohexylamino)propane-1-sulfonic acid (pH 10.5)

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 4, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→85.69 Å / Num. obs: 118811 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rsym value: 0.076 / Net I/σ(I): 28.5
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bacillus circulans T-3040 CITase (3WNK)

3wnk


Resolution: 1.85→85.69 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.337 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19046 5907 5 %RANDOM
Rwork0.16575 ---
obs0.167 112028 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.489 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.27 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.85→85.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9522 0 91 889 10502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.029967
X-RAY DIFFRACTIONr_bond_other_d0.0020.029275
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.94813505
X-RAY DIFFRACTIONr_angle_other_deg0.895321381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17151180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69725.117514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.474151700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.281533
X-RAY DIFFRACTIONr_chiral_restr0.0750.21396
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022365
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_it1.1182.1824699
X-RAY DIFFRACTIONr_mcbond_other1.1182.1814698
X-RAY DIFFRACTIONr_mcangle_it1.9163.2645874
X-RAY DIFFRACTIONr_mcangle_other1.9163.2655875
X-RAY DIFFRACTIONr_scbond_it1.4052.3875268
X-RAY DIFFRACTIONr_scbond_other1.4052.3875268
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3483.4957628
X-RAY DIFFRACTIONr_long_range_B_refined4.9918.19912006
X-RAY DIFFRACTIONr_long_range_B_other4.91318.03811854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 391 -
Rwork0.211 7989 -
obs--96.74 %

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