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- PDB-8r56: Crystal structure of GH31 family Sulfoquinovosidase BmSQase in co... -

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Basic information

Entry
Database: PDB / ID: 8r56
TitleCrystal structure of GH31 family Sulfoquinovosidase BmSQase in covalent complex with SQ-aziridine (SQZ)
ComponentsGlycosyl hydrolase, family 31
KeywordsHYDROLASE / Glycoside hydrolase / CAZy family 31 / sulfoquinovose / activity-based probe
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / Sulfoquinovosidase YihQ-like / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / : / Glycosyl hydrolase, family 31
Similarity search - Component
Biological speciesPriestia megaterium DSM 319 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W003805/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Detection of Sulfoquinovosidase Activity in Cell Lysates Using Activity-Based Probes.
Authors: Li, Z. / Pickles, I.B. / Sharma, M. / Melling, B. / Pallasdies, L. / Codee, J.D.C. / Williams, S.J. / Overkleeft, H.S. / Davies, G.J.
History
DepositionNov 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase, family 31
B: Glycosyl hydrolase, family 31
C: Glycosyl hydrolase, family 31
D: Glycosyl hydrolase, family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,08812
Polymers321,9664
Non-polymers1,1218
Water10,575587
1
A: Glycosyl hydrolase, family 31
C: Glycosyl hydrolase, family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,5446
Polymers160,9832
Non-polymers5614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl hydrolase, family 31
D: Glycosyl hydrolase, family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,5446
Polymers160,9832
Non-polymers5614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.524, 194.726, 117.654
Angle α, β, γ (deg.)90.00, 92.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycosyl hydrolase, family 31


Mass: 80491.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium DSM 319 (bacteria) / Gene: BMQ_3646 / Plasmid: pEt28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D5E1T0
#2: Chemical
ChemComp-Y2W / [(1~{S},2~{R},3~{R},4~{S},6~{R})-6-azanyl-2,3,4-tris(oxidanyl)cyclohexyl]methanesulfonic acid


Mass: 241.262 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H15NO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: A crystal of BmSQase was grown using a 30 mg mL-1 protein solution in buffer C, 0.15 uL protein. 0.15 uL mother liquor, the latter comprising 0.2 M KSCN and 20% w/v PEG (polyethylene glycol) ...Details: A crystal of BmSQase was grown using a 30 mg mL-1 protein solution in buffer C, 0.15 uL protein. 0.15 uL mother liquor, the latter comprising 0.2 M KSCN and 20% w/v PEG (polyethylene glycol) 3350 in 0.1 M Bis-TRIS propane buffer pH 7.5. A stock solution of 1 was prepared at 10 mM in mother liquor. Crystals were soaked for 5 min with 0.3 ul of 1 to a final concentration of 3 mM.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.45→74.99 Å / Num. obs: 102876 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.986 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.08 / Rrim(I) all: 0.212 / Χ2: 1.11 / Net I/σ(I): 9.3 / Num. measured all: 737059
Reflection shellResolution: 2.45→2.49 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 1.174 / Num. measured all: 36181 / Num. unique obs: 5135 / CC1/2: 0.637 / Rpim(I) all: 0.474 / Rrim(I) all: 1.267 / Χ2: 1.09 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→62.55 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.865 / SU B: 10.849 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.792 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24405 4989 4.9 %RANDOM
Rwork0.21188 ---
obs0.21347 97274 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.234 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-1.62 Å2
2--0.99 Å20 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.45→62.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21281 0 4 587 21872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01221886
X-RAY DIFFRACTIONr_bond_other_d0.0010.01619424
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.81529805
X-RAY DIFFRACTIONr_angle_other_deg0.5681.74144587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95152683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.528590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.226103271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1780.23154
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226251
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025273
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_it2.8823.06910741
X-RAY DIFFRACTIONr_mcbond_other2.8813.06910741
X-RAY DIFFRACTIONr_mcangle_it4.3235.51213421
X-RAY DIFFRACTIONr_mcangle_other4.3235.51213422
X-RAY DIFFRACTIONr_scbond_it3.0633.18511145
X-RAY DIFFRACTIONr_scbond_other3.0633.18511143
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7275.77316385
X-RAY DIFFRACTIONr_long_range_B_refined6.20628.4424078
X-RAY DIFFRACTIONr_long_range_B_other6.19528.4624040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 380 -
Rwork0.28 7228 -
obs--99.92 %

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