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- PDB-8eq0: Escherichia coli pyruvate kinase G381A -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8eq0
TitleEscherichia coli pyruvate kinase G381A
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 / phosphorylation / 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
GLYCINE / Pyruvate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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 7, 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
B: Pyruvate kinase
A: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7634
Polymers101,6132
Non-polymers1502
Water1,60389
1
B: Pyruvate kinase
A: Pyruvate kinase
hetero molecules

B: Pyruvate kinase
A: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,5268
Polymers203,2254
Non-polymers3004
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area8010 Å2
ΔGint-38 kcal/mol
Surface area68130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.513, 247.045, 130.231
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: 50806.352 Da / Num. of mol.: 2 / Mutation: G381A
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-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.95 Å3/Da / Density % sol: 58.29 %
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 Sodium HEPES; 1.0M MOPS (acid)), 30% v/v (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: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.62→48.09 Å / Num. obs: 35719 / % possible obs: 97.76 % / Redundancy: 7.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.1913 / Net I/σ(I): 7.11
Reflection shellResolution: 2.62→2.716 Å / Mean I/σ(I) obs: 1.78 / Num. unique obs: 2799 / CC1/2: 0.515

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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: 2.62→48.09 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 1754 4.91 %
Rwork0.2023 33965 -
obs0.2039 35719 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.09 Å2 / Biso mean: 31.6102 Å2 / Biso min: 11.38 Å2
Refinement stepCycle: final / Resolution: 2.62→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 0 17 89 7038
Biso mean--32.94 30 -
Num. residues----924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.62-2.690.3298950.29511899199472
2.69-2.770.29781230.256826382761100
2.77-2.860.25871560.242826312787100
2.86-2.960.27911390.234926182757100
2.96-3.080.28311290.242826422771100
3.08-3.220.32821330.265926462779100
3.22-3.390.2861330.239826802813100
3.39-3.610.23441490.211426232772100
3.61-3.880.24071240.198526852809100
3.88-4.270.21361430.177126652808100
4.27-4.890.19551380.149726772815100
4.89-6.160.16651330.181127442877100
6.16-48.090.20691590.178328172976100

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