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- PDB-4kct: Pyruvate kinase (PYK) from Trypanosoma brucei soaked with Oxaloacetate -

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Basic information

Entry
Database: PDB / ID: 4kct
TitlePyruvate kinase (PYK) from Trypanosoma brucei soaked with Oxaloacetate
ComponentsPyruvate kinase 1
KeywordsTRANSFERASE / pyruvate kinase / decarboxylase
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / phosphorylation / magnesium ion binding / ATP binding
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 / : / PYRUVIC ACID / Pyruvate kinase 1
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhong, W. / Morgan, H.P. / McNae, I.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
CitationJournal: Biochem.J. / Year: 2014
Title: Pyruvate kinases have an intrinsic and conserved decarboxylase activity.
Authors: Zhong, W. / Morgan, H.P. / Nowicki, M.W. / McNae, I.W. / Yuan, M. / Bella, J. / Michels, P.A. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Pyruvate kinase 1
A: Pyruvate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,33913
Polymers109,0792
Non-polymers1,25911
Water14,070781
1
B: Pyruvate kinase 1
A: Pyruvate kinase 1
hetero molecules

B: Pyruvate kinase 1
A: Pyruvate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,67726
Polymers218,1584
Non-polymers2,51922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area21260 Å2
ΔGint-140 kcal/mol
Surface area72050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.990, 108.170, 264.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-1452-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules BA

#1: Protein Pyruvate kinase 1 / / PK 1


Mass: 54539.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PYK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P30615, 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 , 5 types, 790 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-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 15-20% PEG 8,000, 10-20% glycerol, 80 uM F26BP, 800 uM Ponceau S, 50 mM TEA buffer, 100 mM KCl, 50 mM MgCl2, 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: 0.98
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→74.59 Å / Num. all: 107112 / Num. obs: 107112 / % possible obs: 99.6 % / Observed criterion σ(F): 3.6 / Observed criterion σ(I): 3.6
Reflection shellResolution: 1.95→2.06 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→68.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.333 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.108 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18308 5349 5 %RANDOM
Rwork0.15293 ---
obs0.15443 101756 99.6 %-
all-101756 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→68.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7596 0 74 781 8451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197849
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.97310638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82651024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71624.329328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.405151411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2521556
X-RAY DIFFRACTIONr_chiral_restr0.0970.21244
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215808
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 365 -
Rwork0.203 6869 -
obs--95.18 %
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)
16.9187-4.7856-6.85813.66825.03547.0395-0.1268-0.10050.2776-0.10270.2384-0.0106-0.02650.2228-0.11160.1095-0.0855-0.10510.09220.05960.12115.5377-14.124725.69
20.42480.32450.08780.4148-0.08770.1626-0.02130.0468-0.16290.01820.0498-0.1337-0.0386-0.0095-0.02850.03750.028-0.00770.0508-0.00870.097534.2781-27.432441.7099
30.24430.34710.32733.2606-2.00512.65020.0442-0.0499-0.0543-0.49270.091-0.01530.5572-0.2041-0.13530.1754-0.0442-0.05730.02520.01270.038815.9461-46.236263.3184
40.25360.13690.05590.2659-0.08410.14070.0347-0.0154-0.05220.0411-0.0376-0.0481-0.005-0.02410.00290.0660.0061-0.03430.05330.00410.032321.4845-24.306748.6791
50.4244-0.06460.00080.5703-0.09040.01560.01280.0132-0.02440.0053-0.0184-0.06310.0003-0.00240.00560.03240.0013-0.01060.0751-0.01120.046429.4953-2.211938.3754
63.81064.3529-2.69967.609-5.08523.4330.1525-0.26540.2524-0.1546-0.07380.16660.1420.027-0.07870.0786-0.0240.00360.0896-0.0240.03824.1681-14.821450.5284
70.5372-0.00010.19790.11850.12940.23340.0253-0.0537-0.1748-0.01630.0030.0513-0.0331-0.001-0.02840.066-0.01450.00680.01970.00250.0996-10.2485-42.74934.2187
81.521-0.61860.02751.1565-0.53540.916-0.0436-0.09150.0911-0.0780.0011-0.00070.10550.08960.04250.06060.0112-0.0060.0602-0.02220.024716.7918-41.54578.6766
90.33970.10270.0010.16570.12460.1391-0.01460.0373-0.0575-0.0104-0.00010.0099-0.02730.00850.01470.07220.0067-0.01520.0484-0.02190.0343-2.2399-32.209927.2907
100.456-0.296-0.11830.63550.05790.0322-0.01850.0128-0.0780.01220.00090.07590.00180.00180.01760.046-0.0045-0.00320.0602-0.00580.0503-22.1266-19.987237.6695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 14
2X-RAY DIFFRACTION2A15 - 87
3X-RAY DIFFRACTION3A88 - 189
4X-RAY DIFFRACTION4A190 - 357
5X-RAY DIFFRACTION5A358 - 499
6X-RAY DIFFRACTION6B2 - 14
7X-RAY DIFFRACTION7B15 - 87
8X-RAY DIFFRACTION8B88 - 189
9X-RAY DIFFRACTION9B190 - 357
10X-RAY DIFFRACTION10B358 - 499

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