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- PDB-7agk: Crystal structure of E. coli SF kinase (YihV) in complex with pro... -

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Basic information

Entry
Database: PDB / ID: 7agk
TitleCrystal structure of E. coli SF kinase (YihV) in complex with product sulfofructose phosphate (SFP)
ComponentsSulfofructose kinase
KeywordsTRANSFERASE / sulfofructose / sulfoquinovose / SF kinase / sulfoglycolysis / sulfoEMP pathway
Function / homology
Function and homology information


sulfofructose kinase / 6-deoxy-6-sulfofructose kinase activity / 6-sulfoquinovose(1-) catabolic process / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / carbohydrate phosphorylation / kinase activity / ATP binding / cytosol
Similarity search - Function
Sulfofructose kinase / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
Chem-RAH / Sulfofructose kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 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 22, 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

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Assembly

Deposited unit
D: Sulfofructose kinase
A: Sulfofructose kinase
B: Sulfofructose kinase
C: Sulfofructose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,2917
Polymers131,3194
Non-polymers9733
Water00
1
D: Sulfofructose kinase
C: Sulfofructose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9843
Polymers65,6592
Non-polymers3241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-13 kcal/mol
Surface area24390 Å2
MethodPISA
2
A: Sulfofructose kinase
B: Sulfofructose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3084
Polymers65,6592
Non-polymers6482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-14 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.548, 91.856, 312.142
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22B
13D
23C
14A
24B
15A
25C
16B
26C

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
11ILEILELEULEUDA2 - 2962 - 296
21ILEILELEULEUAB2 - 2962 - 296
12ILEILELEULEUDA2 - 2962 - 296
22ILEILELEULEUBC2 - 2962 - 296
13ILEILELEULEUDA2 - 2962 - 296
23ILEILELEULEUCD2 - 2962 - 296
14METMETPHEPHEAB1 - 2971 - 297
24METMETPHEPHEBC1 - 2971 - 297
15METMETPHEPHEAB1 - 2971 - 297
25METMETPHEPHECD1 - 2971 - 297
16METMETVALVALBC1 - 2981 - 298
26METMETVALVALCD1 - 2981 - 298

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Sulfofructose kinase / SF kinase


Mass: 32829.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yihV, b3883, JW5568 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32143, sulfofructose kinase
#2: Chemical ChemComp-RAH / [(2~{S},3~{S},4~{S},5~{R})-3,4,5-tris(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]methanesulfonic acid / 6-deoxy-6-sulfo-D-fructose 1-phosphate


Mass: 324.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13O11PS / Feature type: SUBJECT OF INVESTIGATION
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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% PEG 1500 w/v, 0.1 M PCTP buffer pH8 (propionic acid, cacodylate, bistris propane)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.97→79.16 Å / Num. obs: 29364 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.916 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.071 / Rrim(I) all: 0.203 / Net I/σ(I): 7 / Num. measured all: 238073 / Scaling rejects: 136
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
2.97-3.158.21.3423790146320.8410.4891.431.9100
8.91-79.166.70.082847312570.8540.0370.09113.999.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AG6

7ag6


Resolution: 2.97→79.01 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.881 / SU B: 22.996 / SU ML: 0.406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 1471 5 %RANDOM
Rwork0.2317 ---
obs0.2343 27821 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 183.12 Å2 / Biso mean: 67.685 Å2 / Biso min: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å20 Å2
2--9.13 Å2-0 Å2
3----7.04 Å2
Refinement stepCycle: final / Resolution: 2.97→79.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8088 0 57 0 8145
Biso mean--62.83 --
Num. residues----1193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138298
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177113
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.63211399
X-RAY DIFFRACTIONr_angle_other_deg1.3181.57716184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20651189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58522.958311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15615926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7921530
X-RAY DIFFRACTIONr_chiral_restr0.0560.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210015
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021835
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D71700.07
12A71700.07
21D72380.07
22B72380.07
31D69000.07
32C69000.07
41A82760.06
42B82760.06
51A78100.07
52C78100.07
61B77600.08
62C77600.08
LS refinement shellResolution: 2.97→3.047 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 102 -
Rwork0.381 1965 -
all-2067 -
obs--100 %

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