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- PDB-8eds: Escherichia coli pyruvate kinase (PykF) P70Q -

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Basic information

Entry
Database: PDB / ID: 8eds
TitleEscherichia coli pyruvate kinase (PykF) P70Q
ComponentsPyruvate kinase
KeywordsTRANSFERASE / Pyruvate kinase / Long term evolution experiment / Kinase
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / magnesium ion binding / ATP binding
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / 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 ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / 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 / Beta Barrel / Mainly Beta
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
DepositionSep 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7854
Polymers101,5932
Non-polymers1922
Water3,369187
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,5708
Polymers203,1854
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area9330 Å2
ΔGint-121 kcal/mol
Surface area68440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.848, 244.357, 131.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Pyruvate kinase


Mass: 50796.312 Da / Num. of mol.: 2 / Mutation: P70T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pykF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2TL68, pyruvate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine), 0.1M (1.0M Imidazole; MES monohydrate (acid)), 30% (40% v/v Glycerol; 20% w/v PEG 4000)

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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: Sep 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→44.8 Å / Num. obs: 72182 / % possible obs: 99.29 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 16.28
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.3418 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6936 / CC1/2: 0.794 / % possible all: 96.64

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Processing

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

4yng


Resolution: 2.1→44.8 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 22.43 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2229 2508 3.47 %
Rwork0.2043 69666 -
obs0.2049 72174 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.12 Å2 / Biso mean: 38.5321 Å2 / Biso min: 18.56 Å2
Refinement stepCycle: final / Resolution: 2.1→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7023 0 10 187 7220
Biso mean--30 35.13 -
Num. residues----937
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.140.34041230.30233620374393
2.14-2.180.28091240.28263821394599
2.18-2.230.33031250.27243835396099
2.23-2.280.27741230.25663842396599
2.28-2.340.29571470.243938243971100
2.34-2.40.28942300.23373789401999
2.4-2.470.26171260.226938443970100
2.47-2.550.24981260.228438884014100
2.55-2.650.24321260.222138443970100
2.65-2.750.24991260.225739014027100
2.75-2.880.21961260.210338744000100
2.88-3.030.24111260.212938974023100
3.03-3.220.22561260.220739154041100
3.22-3.470.25441250.217939224047100
3.47-3.810.19172520.188737974049100
3.81-4.370.17591250.168739304055100
4.37-5.50.18161260.15739974123100
5.5-44.80.18521260.17734126425299

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