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- PDB-7ag4: Crystal structure of active site mutant of SQ Isomerase (YihS-H24... -

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Basic information

Entry
Database: PDB / ID: 7ag4
TitleCrystal structure of active site mutant of SQ Isomerase (YihS-H248A) from Salmonella enterica in complex with sulfofructose (SF)
ComponentsSulfoquinovose isomerase
KeywordsISOMERASE / sulfofructose / sulfoquinovose / SQ isomerase / sulfoglycolysis
Function / homology
Function and homology information


sulfoquinovose isomerase / sulfoquinovose isomerase activity / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / carbohydrate metabolic process
Similarity search - Function
Sulfoquinovose isomerase / AGE domain / N-acylglucosamine 2-epimerase/Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
6-deoxy-6-sulfo-D-fructose / Sulfoquinovose isomerase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 Å
AuthorsSharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2017-190 United Kingdom
CitationJournal: Acs Cent.Sci. / Year: 2021
Title: Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis.
Authors: Sharma, M. / Abayakoon, P. / Epa, R. / Jin, Y. / Lingford, J.P. / Shimada, T. / Nakano, M. / Mui, J.W. / Ishihama, A. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.
History
DepositionSep 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfoquinovose isomerase
B: Sulfoquinovose isomerase
D: Sulfoquinovose isomerase
F: Sulfoquinovose isomerase
C: Sulfoquinovose isomerase
E: Sulfoquinovose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,60412
Polymers298,1386
Non-polymers1,4656
Water12,358686
1
A: Sulfoquinovose isomerase
D: Sulfoquinovose isomerase
F: Sulfoquinovose isomerase
hetero molecules

B: Sulfoquinovose isomerase
C: Sulfoquinovose isomerase
E: Sulfoquinovose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,60412
Polymers298,1386
Non-polymers1,4656
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area13470 Å2
ΔGint-54 kcal/mol
Surface area76000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.818, 136.827, 230.036
Angle α, β, γ (deg.)90.000, 95.350, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13A
23F
14A
24C
15A
25E
16B
26D
17B
27F
18B
28C
19B
29E
110D
210F
111D
211C
112D
212E
113F
213C
114F
214E
115C
215E

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
11METMETALAALAAA1 - 41221 - 432
21METMETALAALABB1 - 41221 - 432
12METMETALAALAAA1 - 41221 - 432
22METMETALAALADC1 - 41221 - 432
13METMETLYSLYSAA1 - 41321 - 433
23METMETLYSLYSFD1 - 41321 - 433
14METMETALAALAAA1 - 41221 - 432
24METMETALAALACE1 - 41221 - 432
15METMETALAALAAA1 - 41221 - 432
25METMETALAALAEF1 - 41221 - 432
16GLYGLYALAALABB-2 - 41218 - 432
26GLYGLYALAALADC-2 - 41218 - 432
17SERSERLYSLYSBB-1 - 41319 - 433
27SERSERLYSLYSFD-1 - 41319 - 433
18GLYGLYALAALABB-2 - 41218 - 432
28GLYGLYALAALACE-2 - 41218 - 432
19GLYGLYALAALABB-2 - 41218 - 432
29GLYGLYALAALAEF-2 - 41218 - 432
110SERSERALAALADC-1 - 41219 - 432
210SERSERALAALAFD-1 - 41219 - 432
111HISHISLYSLYSDC-11 - 4139 - 433
211HISHISLYSLYSCE-11 - 4139 - 433
112HISHISLYSLYSDC-11 - 4139 - 433
212HISHISLYSLYSEF-11 - 4139 - 433
113SERSERALAALAFD-1 - 41219 - 432
213SERSERALAALACE-1 - 41219 - 432
114SERSERALAALAFD-1 - 41219 - 432
214SERSERALAALAEF-1 - 41219 - 432
115HISHISLYSLYSCE-11 - 4139 - 433
215HISHISLYSLYSEF-11 - 4139 - 433

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Sulfoquinovose isomerase / SQ isomerase


Mass: 49689.734 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: yihS, STM4021 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8ZKT7, sulfoquinovose isomerase
#2: Chemical
ChemComp-RB8 / 6-deoxy-6-sulfo-D-fructose / [(2~{S},3~{S},4~{S},5~{R})-5-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxolan-2-yl]methanesulfonic acid


Mass: 244.220 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H12O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG 3350, 0.1 M Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.13→53.13 Å / Num. obs: 150876 / % possible obs: 100 % / Redundancy: 4.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.06 / Rrim(I) all: 0.127 / Net I/σ(I): 7.2 / Num. measured all: 653136 / Scaling rejects: 798
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.13-2.174.20.5123116874660.8140.2890.592.399.9
11.67-53.1340.05538549560.990.0320.06414.798.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZBL

2zbl


Resolution: 2.13→52.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.083 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 7611 5 %RANDOM
Rwork0.1805 ---
obs0.1815 143172 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.67 Å2 / Biso mean: 29.737 Å2 / Biso min: 17.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å22.55 Å2
2---0.13 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 2.13→52.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19937 0 90 686 20713
Biso mean--33.12 30.1 -
Num. residues----2502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01320664
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718257
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.63328208
X-RAY DIFFRACTIONr_angle_other_deg1.3961.57941763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52952492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.16221.8861140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.794153012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.65115124
X-RAY DIFFRACTIONr_chiral_restr0.080.22548
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025183
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A146320.05
12B146320.05
21A145700.05
22D145700.05
31A140750.05
32F140750.05
41A145720.04
42C145720.04
51A141250.04
52E141250.04
61B147280.04
62D147280.04
71B140630.05
72F140630.05
81B145910.05
82C145910.05
91B142060.04
92E142060.04
101D140480.04
102F140480.04
111D148590.04
112C148590.04
121D145160.04
122E145160.04
131F139750.05
132C139750.05
141F139500.04
142E139500.04
151C144720.04
152E144720.04
LS refinement shellResolution: 2.13→2.185 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 575 -
Rwork0.248 10583 -
all-11158 -
obs--99.88 %

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