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- PDB-6k0k: Crystal structure of Escherichia coli pyruvate kinase II -

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Basic information

Entry
Database: PDB / ID: 6k0k
TitleCrystal structure of Escherichia coli pyruvate kinase II
ComponentsPyruvate kinase
KeywordsBIOSYNTHETIC PROTEIN / pyruvate kinase
Function / homology
Function and homology information


pyruvate kinase complex / pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / magnesium ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
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 / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Pyruvate kinase / Pyruvate kinase II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsZhao, C.H. / Zhang, Y.P. / Li, Y.
CitationJournal: To Be Published
Title: Crystal structure of Escherichia coli pyruvate kinase II
Authors: Zhao, C.H. / Zhang, Y.P. / Li, Y.
History
DepositionMay 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)210,64311
Polymers209,9694
Non-polymers6747
Water4,396244
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2014
Polymers104,9842
Non-polymers2162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-25 kcal/mol
Surface area38340 Å2
MethodPISA
2
C: Pyruvate kinase
D: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4427
Polymers104,9842
Non-polymers4575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-31 kcal/mol
Surface area33250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.693, 137.300, 139.221
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein
Pyruvate kinase /


Mass: 52492.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: C3T5U7, UniProt: P21599*PLUS, pyruvate kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 6% v/v Tacsimate TM pH 7.0, 0.1M HEPES pH 7.2, 8% w/v Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 63484 / % possible obs: 99 % / Redundancy: 4.5 % / Biso Wilson estimate: 51.5 Å2 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.068 / Net I/σ(I): 8
Reflection shellResolution: 2.68→2.73 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 3135 / Rpim(I) all: 0.478 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+28 / Resolution: 2.68→32.95 Å / SU ML: 0.3588 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.5973 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3098 4.91 %RANDOM
Rwork0.2099 60045 --
obs0.2124 63143 98.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.07 Å2
Refinement stepCycle: LAST / Resolution: 2.68→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13031 0 43 252 13326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008513190
X-RAY DIFFRACTIONf_angle_d1.087717813
X-RAY DIFFRACTIONf_chiral_restr0.05562144
X-RAY DIFFRACTIONf_plane_restr0.00562324
X-RAY DIFFRACTIONf_dihedral_angle_d15.72968169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.720.33391310.2792657X-RAY DIFFRACTION97.79
2.72-2.760.32961260.2592744X-RAY DIFFRACTION99.79
2.76-2.810.3241450.25422723X-RAY DIFFRACTION99.72
2.81-2.860.29971290.24892747X-RAY DIFFRACTION99.9
2.86-2.920.31641550.24072729X-RAY DIFFRACTION99.9
2.92-2.980.31551470.2472702X-RAY DIFFRACTION99.79
2.98-3.040.32461440.24712758X-RAY DIFFRACTION99.76
3.04-3.110.29881460.23472749X-RAY DIFFRACTION99.86
3.11-3.190.30941580.23662686X-RAY DIFFRACTION99.2
3.19-3.280.2842970.22022677X-RAY DIFFRACTION96.05
3.28-3.370.2761570.21812739X-RAY DIFFRACTION99.55
3.37-3.480.2841320.22232754X-RAY DIFFRACTION99.65
3.48-3.610.26671730.20762703X-RAY DIFFRACTION99.45
3.61-3.750.23221420.192743X-RAY DIFFRACTION99.45
3.75-3.920.23451440.1892767X-RAY DIFFRACTION99.45
3.92-4.130.25141170.18532763X-RAY DIFFRACTION99.28
4.13-4.380.20821410.17852748X-RAY DIFFRACTION98.74
4.38-4.720.22631370.16992726X-RAY DIFFRACTION98.01
4.72-5.20.23141430.18782776X-RAY DIFFRACTION98.92
5.2-5.940.26921440.21532772X-RAY DIFFRACTION98.31
5.94-7.470.27761410.2282737X-RAY DIFFRACTION96.13
7.47-32.950.21411490.21162645X-RAY DIFFRACTION89.44

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