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- PDB-4ks0: Pyruvate kinase (PYK) from Trypanosoma cruzi in the presence of M... -

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Basic information

Entry
Database: PDB / ID: 4ks0
TitlePyruvate kinase (PYK) from Trypanosoma cruzi in the presence of Magnesium, oxalate and F26BP
ComponentsPyruvate kinase
KeywordsTRANSFERASE / Tetramer / Pyruvate Kinase / Allostery
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / cellular response to insulin stimulus / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / 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, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,6-di-O-phosphono-beta-D-fructofuranose / : / OXALATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMorgan, H.P. / Zhong, W. / McNae, I.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
CitationJournal: R Soc Open Sci / Year: 2014
Title: Structures of pyruvate kinases display evolutionarily divergent allosteric strategies.
Authors: Morgan, H.P. / Zhong, W. / McNae, I.W. / Michels, P.A. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
History
DepositionMay 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,67710
Polymers113,6942
Non-polymers9838
Water4,576254
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,35420
Polymers227,3884
Non-polymers1,96616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Buried area20260 Å2
ΔGint-133 kcal/mol
Surface area71400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.767, 173.767, 211.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-1193-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Pyruvate kinase /


Mass: 56847.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053511281.60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4D9Z4, pyruvate kinase
#5: Sugar ChemComp-FDP / 2,6-di-O-phosphono-beta-D-fructofuranose / FRUCTOSE-2,6-DIPHOSPHATE / 2,6-di-O-phosphono-beta-D-fructose / 2,6-di-O-phosphono-D-fructose / 2,6-di-O-phosphono-fructose / Fructose 2,6-bisphosphate


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf2PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 260 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9757 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9757 Å / Relative weight: 1
ReflectionResolution: 2.8→55.9 Å / Num. obs: 40095 / % possible obs: 100 % / Observed criterion σ(I): 20.1
Reflection shellResolution: 2.8→2.95 Å / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→55.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.738 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.515 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21627 2010 5 %RANDOM
Rwork0.17388 ---
obs0.17608 38066 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.013 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→55.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7399 0 56 254 7709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197580
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.97610254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3145968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33624.334323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.587151366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4891554
X-RAY DIFFRACTIONr_chiral_restr0.0770.21185
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215615
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 133 -
Rwork0.287 2557 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8151.52566.50755.22262.62767.45850.42160.1561-0.0568-0.0141-0.328-0.28190.42140.0996-0.09350.52920.034-0.00020.13450.00130.225411.730944.34714.3248
20.9902-0.3341-0.73420.2972-0.04841.37170.07670.0171-0.1403-0.0344-0.08090.2579-0.08020.02920.00420.3271-0.06110.03790.1099-0.09230.4981-10.585619.725526.9778
34.3284-0.48390.02123.1471-2.90312.72310.334-0.28750.14230.49060.03260.4493-0.46030.0316-0.36660.4777-0.0490.31470.0733-0.14140.4526-17.423939.914652.8106
40.26910.07290.16530.7909-0.240.29950.0305-0.01190.00780.1223-0.14380.16180.02270.00190.11320.4032-0.04280.06470.1368-0.05130.3695-3.27629.435335.3183
50.8065-0.090.02940.27970.18470.1614-0.01820.064-0.07280.0593-0.0230.12890.00970.04510.04120.4402-0.02860.00460.1219-0.02230.326814.953816.178623.3327
68.61694.2301-2.34722.0839-1.15490.6463-0.18870.20190.2285-0.06970.16930.11710.0527-0.07550.01940.33750.02680.05240.3805-0.04070.243541.84241.54438.644
70.5744-0.27940.4420.42050.0480.7743-0.0185-0.1456-0.0544-0.05140.02240.07130.1681-0.0827-0.00390.429-0.13030.05750.3221-0.02370.190363.79520.19120.777
81.01520.42551.97920.88461.4134.39240.3074-0.0573-0.06230.10690.1081-0.26220.6471-0.014-0.41550.54960.0380.00940.172-0.01810.201476.65844.0573.487
90.1611-0.2160.11280.38490.00640.43910.022-0.00030.023-0.0422-0.02770.00850.1474-0.03580.00560.3787-0.0490.01930.3315-0.01150.185956.82231.78414.733
100.4567-0.1019-0.1120.2275-0.02080.2801-0.0149-0.04010.037-0.06220.04680.00130.128-0.092-0.03180.2117-0.0766-0.00630.4398-0.00790.244738.38616.12522.943
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 14
2X-RAY DIFFRACTION2A15 - 87
3X-RAY DIFFRACTION3A88 - 189
4X-RAY DIFFRACTION4A190 - 357
5X-RAY DIFFRACTION5A358 - 499
6X-RAY DIFFRACTION6B1 - 14
7X-RAY DIFFRACTION7B15 - 87
8X-RAY DIFFRACTION8B88 - 189
9X-RAY DIFFRACTION9B190 - 357
10X-RAY DIFFRACTION10B358 - 499

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