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- PDB-7agh: Crystal structure of SF kinase YihV from E. coli in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7agh
TitleCrystal structure of SF kinase YihV from E. coli in complex with AMPPNP-Mg
ComponentsSulfofructose kinase
KeywordsTRANSFERASE / sulfofructose / SF kinase / carbohydrate kinase / sulfoglycolysis
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Sulfofructose kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsSharma, M. / Davies, G.J. / Jin, Y.
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)133,41711
Polymers131,3194
Non-polymers2,0987
Water64936
1
C: Sulfofructose kinase
B: Sulfofructose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6965
Polymers65,6592
Non-polymers1,0373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-33 kcal/mol
Surface area21780 Å2
MethodPISA
2
A: Sulfofructose kinase
hetero molecules

D: Sulfofructose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7206
Polymers65,6592
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_355-x-3/2,-y,z+1/21
Buried area4780 Å2
ΔGint-42 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.085, 82.224, 170.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12C
22A
13C
23B
14D
24A
15D
25B
16A
26B

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 1 - 296 / Label seq-ID: 1 - 296

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11CA
21DB
12CA
22AC
13CA
23BD
14DB
24AC
15DB
25BD
16AC
26BD

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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350w/v, 0.2 M MgCl2.6H2O, 0.1 M BisTris pH5.5

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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 EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.93→59.21 Å / Num. obs: 25634 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.05 / Rrim(I) all: 0.129 / Net I/σ(I): 10.4 / Num. measured all: 165747 / Scaling rejects: 335
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
2.93-3.116.50.3672634240690.9580.1560.3994.7100
8.79-59.215.60.056598610710.9960.0260.06116.399.5

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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: 2.93→59.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.89 / SU B: 17.156 / SU ML: 0.324 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 1267 5 %RANDOM
Rwork0.2142 ---
obs0.2163 24310 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: 102.55 Å2 / Biso mean: 39.025 Å2 / Biso min: 0.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å2-0 Å20 Å2
2--4.43 Å2-0 Å2
3----1.6 Å2
Refinement stepCycle: final / Resolution: 2.93→59.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8364 0 127 36 8527
Biso mean--44.99 23.29 -
Num. residues----1182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138654
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177750
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.63611873
X-RAY DIFFRACTIONr_angle_other_deg1.291.57617675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52151176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4622.779349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.697151111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.781537
X-RAY DIFFRACTIONr_chiral_restr0.0560.21210
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021905
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C87410.06
12D87410.06
21C84580.08
22A84580.08
31C82250.08
32B82250.08
41D84240.08
42A84240.08
51D82370.08
52B82370.08
61A83570.07
62B83570.07
LS refinement shellResolution: 2.93→3.006 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 103 -
Rwork0.269 1756 -
all-1859 -
obs--100 %

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