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- PDB-8eu4: Escherichia coli pyruvate kinase A301S -

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Basic information

Entry
Database: PDB / ID: 8eu4
TitleEscherichia coli pyruvate kinase A301S
ComponentsPyruvate kinase
KeywordsTRANSFERASE / Pyruvate kinase / Long term evolution experiment / Kinase
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / phosphorylation / kinase activity / magnesium ion binding / ATP binding
Similarity search - Function
Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily ...Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDonovan, K.A. / Coombes, D. / Dobson, R.C.J. / Cooper, T.F.
Funding support United States, 2items
OrganizationGrant numberCountry
Other governmentUS Army Research Office W911NF-11-1-0481
National Science Foundation (NSF, United States)DEB-1253650 United States
CitationJournal: To Be Published
Title: Beneficial mutations occurring in E. coli pyruvate kinase afford new allosteric mechanisms leading to faster resumption of growth
Authors: Donovan, K.A. / Coombes, D. / Dobson, R.C.J. / Cooper, T.F.
History
DepositionOct 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyruvate kinase
E: Pyruvate kinase
D: Pyruvate kinase
G: Pyruvate kinase
B: Pyruvate kinase
F: Pyruvate kinase
H: Pyruvate kinase
C: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,23516
Polymers406,4678
Non-polymers7698
Water19,2041066
1
A: Pyruvate kinase
D: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,6188
Polymers203,2334
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-122 kcal/mol
Surface area67940 Å2
MethodPISA
2
E: Pyruvate kinase
G: Pyruvate kinase
F: Pyruvate kinase
H: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,6188
Polymers203,2334
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-119 kcal/mol
Surface area67830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.334, 74.473, 240.826
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyruvate kinase


Mass: 50808.324 Da / Num. of mol.: 8 / Mutation: A301S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EL79_2019, EL80_2048 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A0G552, pyruvate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1066 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M (Malic acid, MES, Tris), 25 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.08
ReflectionResolution: 2.1→48.17 Å / Num. obs: 267878 / % possible obs: 99.99 % / Redundancy: 2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06029 / Net I/σ(I): 11.61
Reflection shellResolution: 2.1→2.175 Å / Mean I/σ(I) obs: 2.16 / Num. unique obs: 26557 / CC1/2: 0.734 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YNG

4yng


Resolution: 2.1→48.17 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.64 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2236 13639 5.09 %
Rwork0.202 254239 -
obs0.2037 267878 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.9 Å2 / Biso mean: 30.7377 Å2 / Biso min: 3.89 Å2
Refinement stepCycle: final / Resolution: 2.1→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27730 0 40 1066 28836
Biso mean--26.63 28.61 -
Num. residues----3695
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.130.1817350.1541122141294992
2.13-2.170.19326380.155126311326995
2.17-2.220.19167080.1588126131332195
2.22-2.260.19266500.1608127621341295
2.26-2.310.2027380.171125781331694
2.31-2.360.19497070.1656125731328095
2.36-2.420.21746850.1737127051339095
2.42-2.490.20256770.1725127621343995
2.49-2.560.2266480.1817126541330295
2.56-2.640.20366130.1772127241333795
2.64-2.740.20817270.1858126751340295
2.74-2.850.20936700.1908126961336695
2.85-2.980.23586970.2032127051340295
2.98-3.130.23756560.2125127391339595
3.13-3.330.23976830.2225127381342195
3.33-3.590.2566570.2291127981345595
3.59-3.950.2486690.2341128031347295
3.95-4.520.23617670.2247127051347294
4.52-5.690.21496640.2042129501361495
5.69-48.170.23396500.2288132141386495

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