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- PDB-7ag1: Crystal structure of E. coli SFP aldolase (YihT) from sulfo-EMP p... -

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Basic information

Entry
Database: PDB / ID: 7ag1
TitleCrystal structure of E. coli SFP aldolase (YihT) from sulfo-EMP pathway
ComponentsSulfofructosephosphate aldolase
KeywordsLYASE / sulfofructose phosphate / SFP aldolase / sulfoglycolysis / sulfolactaldehyde / sulfoEMP
Function / homology
Function and homology information


sulfofructosephosphate aldolase / 6-deoxy-6-sulfofructose-1-phosphate aldolase activity / 6-sulfoquinovose(1-) catabolic process / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde
Similarity search - Function
Sulfofructosephosphate aldolase, YihT / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
Sulfofructosephosphate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 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

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Assembly

Deposited unit
Z: Sulfofructosephosphate aldolase
X: Sulfofructosephosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,74111
Polymers66,1822
Non-polymers5599
Water7,026390
1
Z: Sulfofructosephosphate aldolase
X: Sulfofructosephosphate aldolase
hetero molecules

Z: Sulfofructosephosphate aldolase
X: Sulfofructosephosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,48222
Polymers132,3654
Non-polymers1,11718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9330 Å2
ΔGint35 kcal/mol
Surface area47020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.166, 155.827, 89.624
Angle α, β, γ (deg.)90.000, 102.900, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Z
21X

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 2 - 293 / Label seq-ID: 2 - 293

Dom-IDAuth asym-IDLabel asym-ID
1ZA
2XB

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Components

#1: Protein Sulfofructosephosphate aldolase / SFP aldolase


Mass: 33091.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yihT, b3881, JW3852 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P32141, sulfofructosephosphate aldolase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.25 M sodium nitrate, 0.1 M BisTris 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: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→47.5 Å / Num. obs: 46029 / % possible obs: 100 % / Redundancy: 4.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.078 / Rrim(I) all: 0.165 / Net I/σ(I): 7 / Num. measured all: 195045 / Scaling rejects: 42
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
2-2.054.10.9551377033930.6810.5321.0961.8100
8.94-47.54.40.04923135280.9940.0260.05617.899.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
Aimless0.5.29data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TO3

1to3


Resolution: 2→47 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.576 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 2261 4.9 %RANDOM
Rwork0.1861 ---
obs0.1875 43765 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.02 Å2 / Biso mean: 26.054 Å2 / Biso min: 6.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å2-0 Å21.24 Å2
2---2.92 Å2-0 Å2
3---1.46 Å2
Refinement stepCycle: final / Resolution: 2→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4483 0 36 421 4940
Biso mean--42.37 33.44 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134619
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174508
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6346246
X-RAY DIFFRACTIONr_angle_other_deg1.3581.58110356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78522.393234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73615789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6861534
X-RAY DIFFRACTIONr_chiral_restr0.0730.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025314
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021016
Refine LS restraints NCS

Ens-ID: 1 / Number: 9331 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1Z
2X
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 199 -
Rwork0.271 3180 -
all-3379 -
obs--99.97 %

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