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- PDB-8eq3: Escherichia coli pyruvate kinase A301T -

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Basic information

Entry
Database: PDB / ID: 8eq3
TitleEscherichia coli pyruvate kinase A301T
ComponentsPyruvate kinase
KeywordsTRANSFERASE / Pyruvate kinase / Long term evolution experiment / Kinase
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / phosphorylation / 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
IMIDAZOLE / MALONATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1107
Polymers101,6452
Non-polymers4655
Water16,141896
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,22014
Polymers203,2894
Non-polymers93110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area10770 Å2
ΔGint-94 kcal/mol
Surface area68200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.219, 247.074, 130.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-964-

HOH

21A-1084-

HOH

31B-1009-

HOH

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Components

#1: Protein Pyruvate kinase


Mass: 50822.348 Da / Num. of mol.: 2 / Mutation: A301T
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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M (Malonic acid, Imidazole, Boric acid), 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: Mar 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.01→55.85 Å / Num. obs: 80594 / % possible obs: 99.09 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0415 / Net I/σ(I): 13.63
Reflection shellResolution: 2.01→2.082 Å / Rmerge(I) obs: 0.3238 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7347 / CC1/2: 0.753

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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: 2.01→55.85 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.83 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1982 4046 5.02 %
Rwork0.1622 76548 -
obs0.164 80594 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.09 Å2 / Biso mean: 30.2407 Å2 / Biso min: 11.13 Å2
Refinement stepCycle: final / Resolution: 2.01→55.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6969 0 38 896 7903
Biso mean--38.59 36.11 -
Num. residues----929
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.030.3041940.29231878197271
2.03-2.060.32811020.24772538264095
2.06-2.080.23791360.21712638277499
2.08-2.110.24481510.203425892740100
2.11-2.140.25361420.180626502792100
2.14-2.170.22031570.177326372794100
2.17-2.20.2281600.168726212781100
2.2-2.240.21231450.171326472792100
2.24-2.270.20141510.168226382789100
2.27-2.310.20571190.163326552774100
2.31-2.350.18961220.163927112833100
2.35-2.40.19411370.151826112748100
2.4-2.450.22141460.15426662812100
2.45-2.50.23271380.151526632801100
2.5-2.560.18821500.148326332783100
2.56-2.620.19831380.145326682806100
2.62-2.690.20861460.152326692815100
2.69-2.770.20911290.15326622791100
2.77-2.860.20521610.163526372798100
2.86-2.960.18831500.160226602810100
2.96-3.080.20361520.170126602812100
3.08-3.220.20791400.164827012841100
3.22-3.390.24081290.166926822811100
3.39-3.610.20811390.162626942833100
3.61-3.880.17461370.158726932830100
3.88-4.270.1611410.144127042845100
4.28-4.890.16511270.128327382865100
4.89-6.160.15171500.150527532903100
6.16-55.850.18271570.178728523009100

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