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- PDB-8edt: E. coli Pyruvate kinase (PykF) T462I -

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Basic information

Entry
Database: PDB / ID: 8edt
TitleE. coli Pyruvate kinase (PykF) T462I
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: 2.09 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


Theoretical massNumber of molelcules
Total (without water)101,6092
Polymers101,6092
Non-polymers00
Water1,17165
1
A: Pyruvate kinase
B: Pyruvate kinase

A: Pyruvate kinase
B: Pyruvate kinase


Theoretical massNumber of molelcules
Total (without water)203,2184
Polymers203,2184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area8090 Å2
ΔGint-46 kcal/mol
Surface area70020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.680, 247.412, 129.965
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: 50804.379 Da / Num. of mol.: 2 / Mutation: T462I
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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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: 58.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M (0.2M 1,6-Hexanediol; 0.2M 1-Butanol 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1M (Imidazole; MES monohydrate (acid)), 30% v/v (40% v/v ...Details: 0.1 M (0.2M 1,6-Hexanediol; 0.2M 1-Butanol 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1M (Imidazole; MES monohydrate (acid)), 30% v/v (40% v/v Ethylene glycol; 20 % w/v PEG 8000), 100uM 1,8-ANS

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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: Jun 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.09→40.89 Å / Num. obs: 71661 / % possible obs: 99.96 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.69
Reflection shellResolution: 2.09→2.165 Å / Rmerge(I) obs: 0.7768 / Num. unique obs: 7046 / CC1/2: 0.335 / % possible all: 99.97

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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: 2.09→40.89 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 23.12 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2357 3091 4.31 %
Rwork0.2177 68570 -
obs0.2185 71661 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.51 Å2 / Biso mean: 45.5312 Å2 / Biso min: 11.63 Å2
Refinement stepCycle: final / Resolution: 2.09→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6935 0 0 65 7000
Biso mean---30 -
Num. residues----926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.120.27711060.32533062316898
2.12-2.160.33651510.304730953246100
2.16-2.190.34781440.302930663210100
2.19-2.230.32491360.295830913227100
2.23-2.280.29411790.278130283207100
2.28-2.320.30761250.263331253250100
2.32-2.370.26881250.257430693194100
2.37-2.430.24621250.25531173242100
2.43-2.490.28631250.246631573282100
2.49-2.560.27061250.252630633188100
2.56-2.630.25221250.248731053230100
2.63-2.720.24672500.236829913241100
2.72-2.810.25141250.233531373262100
2.81-2.930.26351250.23631073232100
2.93-3.060.29061250.240731333258100
3.06-3.220.30721250.249231403265100
3.22-3.420.23921250.240331523277100
3.42-3.690.21811250.208331483273100
3.69-4.060.24191250.194231723297100
4.06-4.640.18422500.162830533303100
4.64-5.850.19721250.174932083333100
5.85-40.890.17751250.172533513476100

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