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- PDB-5aeg: A bacterial protein structure in glycoside hydrolase family 31. -

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Basic information

Entry
Database: PDB / ID: 5aeg
TitleA bacterial protein structure in glycoside hydrolase family 31.
ComponentsALPHA-GLUCOSIDASE YIHQ
KeywordsHYDROLASE / GH31 / ALPHA-SULFOQUINOVOSIDASE
Function / homology
Function and homology information


sulfoquinovosidase / sulfoquinovosidase activity / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Sulfoquinovosidase YihQ-like / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Sulfoquinovosidase YihQ-like / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5-fluoro-alpha-L-idopyranose / Sulfoquinovosidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJin, Y. / Speciale, G. / Davies, G.J. / Williams, S.J. / Goddard-Borger, E.D.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Yihq is a Sulfoquinovosidase that Cleaves Sulfoquinovosyl Diacylglyceride Sulfolipids.
Authors: Speciale, G. / Jin, Y. / Davies, G.J. / Williams, S.J. / Goddard-Borger, E.D.
History
DepositionAug 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-GLUCOSIDASE YIHQ
B: ALPHA-GLUCOSIDASE YIHQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,59211
Polymers156,8482
Non-polymers7449
Water13,043724
1
A: ALPHA-GLUCOSIDASE YIHQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7766
Polymers78,4241
Non-polymers3525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-GLUCOSIDASE YIHQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8165
Polymers78,4241
Non-polymers3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.665, 112.643, 111.881
Angle α, β, γ (deg.)90.00, 109.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein ALPHA-GLUCOSIDASE YIHQ / ALPHA-SULFOQUINOVOSIDASE


Mass: 78423.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32138, alpha-glucosidase
#5: Sugar ChemComp-B9D / 5-fluoro-alpha-L-idopyranose / (2R,3R,4R,5S,6R)-6-fluoranyl-6-(hydroxymethyl)oxane-2,3,4,5-tetrol / 5-fluoro-alpha-L-idose / 5-fluoro-L-idose / 5-fluoro-idose


Type: L-saccharide, alpha linking / Mass: 198.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H11FO6

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Non-polymers , 4 types, 732 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 724 / 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 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growTemperature: 293 K / pH: 6.5
Details: 25 MG ML-1 YIHQ PROTEIN STOCK IS MIXED WITH EQUAL VOLUME OF PRECIPITANT COMPOSED OF 50-60% (V/V) 2-METHYL-2,4-PENTANEDIOL, 0.1-0.15 M CACL2, AND BIS-TRIS, (PH 6.5) AFTER 3-4 DAYS AT 20 ...Details: 25 MG ML-1 YIHQ PROTEIN STOCK IS MIXED WITH EQUAL VOLUME OF PRECIPITANT COMPOSED OF 50-60% (V/V) 2-METHYL-2,4-PENTANEDIOL, 0.1-0.15 M CACL2, AND BIS-TRIS, (PH 6.5) AFTER 3-4 DAYS AT 20 DEGREE. THE LIGAND I5F WAS SOAKED INTO THE NATIVE CRYSTAL.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→49.68 Å / Num. obs: 154198 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.5
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0095refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AED

5aed


Resolution: 1.85→105.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.877 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 14-17 IN CHAIN A ARE DISORDERED DISORDERED REGIONS WERE NOT MODELED IN.
RfactorNum. reflection% reflectionSelection details
Rfree0.19337 7578 4.9 %RANDOM
Rwork0.16026 ---
obs0.16189 146377 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.762 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20.91 Å2
2---2.36 Å20 Å2
3---2.72 Å2
Refinement stepCycle: LAST / Resolution: 1.85→105.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10757 0 41 724 11522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01911125
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210054
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9315128
X-RAY DIFFRACTIONr_angle_other_deg1.077323122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25951338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1224.304560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.556151759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5341550
X-RAY DIFFRACTIONr_chiral_restr0.130.21563
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212758
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022762
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_it3.2313.3585349
X-RAY DIFFRACTIONr_mcbond_other3.2293.3575348
X-RAY DIFFRACTIONr_mcangle_it4.1645.0186682
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9863.7095776
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.327 555 -
Rwork0.318 10430 -
obs--94.98 %

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