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- PDB-7ofx: Crystal structure of a GH31 family sulfoquinovosidase mutant D455... -

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Basic information

Entry
Database: PDB / ID: 7ofx
TitleCrystal structure of a GH31 family sulfoquinovosidase mutant D455N from Agrobacterium tumefaciens in complex with sulfoquinovosyl glycerol (SQGro)
ComponentsAlpha-glucosidase yihQ
KeywordsHYDROLASE / sulfoquinovose / SQGro / sulfoquinovosyl glycerol / SQDG / sulfoglycolysis / sulfo-EMP
Function / homology
Function and homology information


: / alpha-glucosidase / carbohydrate binding
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
Chem-VCW / Alpha-glucosidase yihQ
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2017-190 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria.
Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / ...Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / Ascher, D.B. / McConville, M.J. / Davies, G.J. / Williams, S.J. / Goddard-Borger, E.D.
History
DepositionMay 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 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: Alpha-glucosidase yihQ
C: Alpha-glucosidase yihQ
D: Alpha-glucosidase yihQ
B: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,1998
Polymers300,9264
Non-polymers1,2734
Water7,909439
1
A: Alpha-glucosidase yihQ
B: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,0994
Polymers150,4632
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alpha-glucosidase yihQ
D: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,0994
Polymers150,4632
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.534, 168.396, 100.687
Angle α, β, γ (deg.)90.000, 116.530, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22D
13A
23B
14C
24D
15C
25B
16D
26B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISLEULEUAA2 - 6602 - 660
21HISHISLEULEUCB2 - 6602 - 660
12METMETLEULEUAA1 - 6601 - 660
22METMETLEULEUDC1 - 6601 - 660
13METMETLEULEUAA1 - 6601 - 660
23METMETLEULEUBD1 - 6601 - 660
14HISHISARGARGCB2 - 6612 - 661
24HISHISARGARGDC2 - 6612 - 661
15HISHISARGARGCB2 - 6612 - 661
25HISHISARGARGBD2 - 6612 - 661
16METMETTHRTHRDC1 - 6621 - 662
26METMETTHRTHRBD1 - 6621 - 662

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Alpha-glucosidase yihQ


Mass: 75231.438 Da / Num. of mol.: 4 / Mutation: D455N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: SY94_3281 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A083ZKV2, alpha-glucosidase
#2: Chemical
ChemComp-VCW / [(2S,3S,4S,5R,6S)-6-[(2R)-2,3-bis(oxidanyl)propoxy]-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid / sulfoquinovosyl glycerol / SQGro


Mass: 318.298 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H18O10S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.49 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 24% PEG 3350 w/v, 0.2 M KSCN, 0.1 M Bis-Tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.15→61.51 Å / Num. obs: 153301 / % possible obs: 97.4 % / Redundancy: 2.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.061 / Rrim(I) all: 0.109 / Net I/σ(I): 8.1 / Num. measured all: 442708 / Scaling rejects: 162
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.9 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.15-2.190.6862236977290.6240.4590.8291.698.9
11.78-61.510.03726669180.9960.0250.04524.692

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OHT

5oht


Resolution: 2.15→61.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.942 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 7734 5 %RANDOM
Rwork0.1942 ---
obs0.1957 145522 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.95 Å2 / Biso mean: 28.618 Å2 / Biso min: 2.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å2-1.76 Å2
2---0.38 Å2-0 Å2
3---1.03 Å2
Refinement stepCycle: final / Resolution: 2.15→61.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20405 0 80 439 20924
Biso mean--22.24 23.37 -
Num. residues----2650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01321076
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718768
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.63728727
X-RAY DIFFRACTIONr_angle_other_deg1.3471.57342948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21552646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46121.31115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.885152973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.65115142
X-RAY DIFFRACTIONr_chiral_restr0.0710.22684
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0224403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025269
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A215760.04
12C215760.04
21A215940.04
22D215940.04
31A215090.05
32B215090.05
41C216110.04
42D216110.04
51C214510.05
52B214510.05
61D215200.06
62B215200.06
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 567 -
Rwork0.293 10906 -
all-11473 -
obs--98.84 %

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