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- PDB-8eq1: Escherichia coli pyruvate kinase D127N -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8eq1
TitleEscherichia coli pyruvate kinase D127N
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase
C: Pyruvate kinase
B: Pyruvate kinase
D: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,5508
Polymers203,1654
Non-polymers3844
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-113 kcal/mol
Surface area70310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.260, 131.755, 129.091
Angle α, β, γ (deg.)90.000, 107.180, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 55 or (resid 56...
21(chain B and (resid 1 through 55 or (resid 56...
31(chain C and (resid 1 through 75 or (resid 76...
41(chain D and (resid 1 through 55 or (resid 56...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSER(chain A and (resid 1 through 55 or (resid 56...AA1 - 551 - 55
12LYSLYSLYSLYS(chain A and (resid 1 through 55 or (resid 56...AA5656
13METMETLEULEU(chain A and (resid 1 through 55 or (resid 56...AA1 - 4701 - 470
14METMETLEULEU(chain A and (resid 1 through 55 or (resid 56...AA1 - 4701 - 470
15METMETLEULEU(chain A and (resid 1 through 55 or (resid 56...AA1 - 4701 - 470
16METMETLEULEU(chain A and (resid 1 through 55 or (resid 56...AA1 - 4701 - 470
21METMETSERSER(chain B and (resid 1 through 55 or (resid 56...BC1 - 551 - 55
22LYSLYSLYSLYS(chain B and (resid 1 through 55 or (resid 56...BC5656
23METMETLEULEU(chain B and (resid 1 through 55 or (resid 56...BC1 - 4701 - 470
24METMETLEULEU(chain B and (resid 1 through 55 or (resid 56...BC1 - 4701 - 470
25METMETLEULEU(chain B and (resid 1 through 55 or (resid 56...BC1 - 4701 - 470
26METMETLEULEU(chain B and (resid 1 through 55 or (resid 56...BC1 - 4701 - 470
31METMETMETMET(chain C and (resid 1 through 75 or (resid 76...CB1 - 751 - 75
32LYSLYSLEULEU(chain C and (resid 1 through 75 or (resid 76...CB76 - 7776 - 77
33METMETLEULEU(chain C and (resid 1 through 75 or (resid 76...CB1 - 4701 - 470
34METMETLEULEU(chain C and (resid 1 through 75 or (resid 76...CB1 - 4701 - 470
35METMETLEULEU(chain C and (resid 1 through 75 or (resid 76...CB1 - 4701 - 470
36METMETLEULEU(chain C and (resid 1 through 75 or (resid 76...CB1 - 4701 - 470
41METMETSERSER(chain D and (resid 1 through 55 or (resid 56...DD1 - 551 - 55
42LYSLYSLYSLYS(chain D and (resid 1 through 55 or (resid 56...DD5656
43METMETLEULEU(chain D and (resid 1 through 55 or (resid 56...DD1 - 4701 - 470
44METMETLEULEU(chain D and (resid 1 through 55 or (resid 56...DD1 - 4701 - 470
45METMETLEULEU(chain D and (resid 1 through 55 or (resid 56...DD1 - 4701 - 470
46METMETLEULEU(chain D and (resid 1 through 55 or (resid 56...DD1 - 4701 - 470

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Components

#1: Protein
Pyruvate kinase


Mass: 50791.340 Da / Num. of mol.: 4 / Mutation: D127N
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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 59.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.12M (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 (1.0M Imidazole; 1.0M MES monohydrate (acid)), 30% v/v ...Details: 0.12M (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 (1.0M Imidazole; 1.0M MES monohydrate (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: Aug 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.32→42.63 Å / Num. obs: 105239 / % possible obs: 99.93 % / Redundancy: 3.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.1054 / Net I/σ(I): 5.84
Reflection shellResolution: 2.32→2.403 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.8385 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 10525 / CC1/2: 0.789 / % possible all: 99.99

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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: 2.32→42.63 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.06 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.224 3340 3.17 %
Rwork0.2075 101899 -
obs0.2081 105239 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.17 Å2 / Biso mean: 50.0655 Å2 / Biso min: 13.41 Å2
Refinement stepCycle: final / Resolution: 2.32→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13884 0 20 88 13992
Biso mean--60.89 38.41 -
Num. residues----1856
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8688X-RAY DIFFRACTION9.518TORSIONAL
12B8688X-RAY DIFFRACTION9.518TORSIONAL
13C8688X-RAY DIFFRACTION9.518TORSIONAL
14D8688X-RAY DIFFRACTION9.518TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.32-2.350.19864000.18083982100
2.35-2.390.18241310.16984276100
2.39-2.430.16894362100
2.43-2.470.16481310.16524231100
2.47-2.510.20971380.17634187100
2.51-2.550.24551290.17534267100
2.55-2.60.17581300.17544221100
2.6-2.660.19761320.17724230100
2.66-2.710.259420.21124424100
2.71-2.780.2591320.21694196100
2.78-2.850.2451340.22574279100
2.85-2.920.24721290.23344253100
2.92-3.010.26211300.24094247100
3.01-3.110.26091330.25374225100
3.11-3.220.22160.25814379100
3.22-3.350.33781360.26224235100
3.35-3.50.27391390.2424289100
3.5-3.680.25621520.24284211100
3.68-3.910.26681710.23394232100
3.91-4.210.18231810.20234199100
4.21-4.640.2287870.17934296100
4.64-5.310.18722160.17874206100
5.31-6.680.23211910.19964227100
6.68-42.630.19412100.1733424599

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