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- PDB-5oht: A GH31 family sulfoquinovosidase from E. coli in complex with aza... -

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Basic information

Entry
Database: PDB / ID: 5oht
TitleA GH31 family sulfoquinovosidase from E. coli in complex with aza-sugar inhibitor IFGSQ
ComponentsSulfoquinovosidase
KeywordsHYDROLASE / sulfoglycosidase / sulfoglycolysis / complex / general acid-base varient
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
Chem-9VH / Sulfoquinovosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsJin, Y. / Williams, S.J. / Goddard-Borger, E. / Davies, G.J.
CitationJournal: ACS Cent Sci / Year: 2018
Title: Structural and Biochemical Insights into the Function and Evolution of Sulfoquinovosidases.
Authors: Abayakoon, P. / Jin, Y. / Lingford, J.P. / Petricevic, M. / John, A. / Ryan, E. / Wai-Ying Mui, J. / Pires, D.E.V. / Ascher, D.B. / Davies, G.J. / Goddard-Borger, E.D. / Williams, S.J.
History
DepositionJul 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Jan 17, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Assembly

Deposited unit
A: Sulfoquinovosidase
B: Sulfoquinovosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,3506
Polymers156,8482
Non-polymers5034
Water11,133618
1
A: Sulfoquinovosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6753
Polymers78,4241
Non-polymers2512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfoquinovosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6753
Polymers78,4241
Non-polymers2512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.473, 86.269, 86.810
Angle α, β, γ (deg.)100.760, 113.770, 97.140
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

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Components

#1: Protein Sulfoquinovosidase / SQase


Mass: 78423.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: yihQ, squQ, b3878, JW3849 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32138, sulfoquinovosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-9VH / [(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methanesulfonic acid


Mass: 211.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 2.9 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25 MG/ML-1 PROTEIN IN 50 MM NAPO4 , PH6.5, AND 250 MM NACL BUFFER 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 20 DEGREE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.87→44.62 Å / Num. obs: 140829 / % possible obs: 97.8 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0378 / Net I/σ(I): 14.8
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6956 / CC1/2: 0.622 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia23.1data reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5aee

5aee


Resolution: 1.87→44.62 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.113
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 6991 5 %RANDOM
Rwork0.166 ---
obs0.1678 140828 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.14 Å2 / Biso mean: 42.6633 Å2 / Biso min: 22.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-1.59 Å20.16 Å2
2---2.68 Å2-0.14 Å2
3---1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.87→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10675 0 28 618 11321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01911027
X-RAY DIFFRACTIONr_bond_other_d00.029598
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.92615004
X-RAY DIFFRACTIONr_angle_other_deg3.8752.99722261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9251335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81324.27548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.399151712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9551549
X-RAY DIFFRACTIONr_chiral_restr0.1160.21557
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112450
X-RAY DIFFRACTIONr_gen_planes_other0.0130.022435
X-RAY DIFFRACTIONr_mcbond_it3.7194.0785343
X-RAY DIFFRACTIONr_mcbond_other3.7194.0785342
X-RAY DIFFRACTIONr_mcangle_it4.6216.0866671
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 515 -
Rwork0.313 9830 -
all-10345 -
obs--96.78 %

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