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- PDB-6lgd: Bombyx mori GH13 sucrose hydrolase complexed with 1,4-dideoxy-1,4... -

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Basic information

Entry
Database: PDB / ID: 6lgd
TitleBombyx mori GH13 sucrose hydrolase complexed with 1,4-dideoxy-1,4-imino-D-arabinitol
ComponentsSucrose hydrolase
KeywordsHYDROLASE / Sucrose / Glycoside hydrolase / GH13 / Inhibitor
Function / homology
Function and homology information


alpha-glucosidase / hydrolase activity, acting on glycosyl bonds / carbohydrate metabolic process / hydrolase activity / metal ion binding
Similarity search - Function
Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
1,4-DIDEOXY-1,4-IMINO-D-ARABINITOL / TRIETHYLENE GLYCOL / alpha-glucosidase / Alpha-glucosidase
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMiyazaki, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science19K15748 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure-function analysis of silkworm sucrose hydrolase uncovers the mechanism of substrate specificity in GH13 subfamily 17exo-alpha-glucosidases.
Authors: Miyazaki, T. / Park, E.Y.
History
DepositionDec 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sucrose hydrolase
B: Sucrose hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,53316
Polymers137,4782
Non-polymers1,05414
Water18,3931021
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-41 kcal/mol
Surface area43640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.054, 146.444, 153.291
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 Sucrose hydrolase


Mass: 68739.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: BmSuh / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A077JI83, UniProt: H9J974*PLUS

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Non-polymers , 6 types, 1035 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1AB / 1,4-DIDEOXY-1,4-IMINO-D-ARABINITOL


Mass: 133.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 8% PEG 3350, 0.2 M magnesium acetate, 10 mM 1,4-dideoxy-1,4-imino-D-arabinitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 148203 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.4
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 21397 / CC1/2: 0.755 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata scaling
XDSdata reduction
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BRQ

5brq


Resolution: 1.75→48.29 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.228 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.089
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 7335 5 %RANDOM
Rwork0.1621 ---
obs0.1632 140585 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.74 Å2 / Biso mean: 28.54 Å2 / Biso min: 19.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å2-0 Å2-0 Å2
2---1.56 Å20 Å2
3---1.08 Å2
Refinement stepCycle: final / Resolution: 1.75→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9302 0 64 1021 10387
Biso mean--40.13 37.16 -
Num. residues----1140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139654
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178391
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.64413141
X-RAY DIFFRACTIONr_angle_other_deg1.3141.57319497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95651142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8122.746568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.617151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.651554
X-RAY DIFFRACTIONr_chiral_restr0.0630.21190
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022172
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 541 -
Rwork0.265 10259 -
all-10800 -
obs--100 %

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