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- PDB-4kcv: Pyruvate kinase (PYK) from Trypanosoma brucei soaked with 2-oxogl... -

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Basic information

Entry
Database: PDB / ID: 4kcv
TitlePyruvate kinase (PYK) from Trypanosoma brucei soaked with 2-oxoglutaric acid
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-OXOGLUTARIC ACID / 2,6-di-O-phosphono-beta-D-fructofuranose / : / Pyruvate kinase 1
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 / 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 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
B: Pyruvate kinase 1
A: Pyruvate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,45513
Polymers109,0792
Non-polymers1,37611
Water13,529751
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)220,90926
Polymers218,1584
Non-polymers2,75122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area21540 Å2
ΔGint-149 kcal/mol
Surface area71800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.250, 108.010, 265.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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, 760 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-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#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.: 751 / 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: 3.4 Å3/Da / Density % sol: 63.79 %
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, 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: I24 / 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: 2.18→74.63 Å / Num. all: 77484 / Num. obs: 77484 / % possible obs: 100 % / Observed criterion σ(F): 3.9 / Observed criterion σ(I): 3.9
Reflection shellResolution: 2.18→2.3 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→74.63 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.704 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.161 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19341 3895 5 %RANDOM
Rwork0.15753 ---
obs0.15934 73586 99.96 %-
all-73586 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.625 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.18→74.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7596 0 82 751 8429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.027809
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.97310568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22951004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69124.356326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.289151398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5631555
X-RAY DIFFRACTIONr_chiral_restr0.1420.21234
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215763
LS refinement shellResolution: 2.18→2.239 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 287 -
Rwork0.19 5101 -
obs--99.78 %
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)
15.634-2.7356-5.45751.87022.84695.3635-0.039-0.15530.2195-0.22530.18860.0477-0.05070.2036-0.14950.1123-0.0502-0.07430.07060.02920.0615.5817-14.223525.8841
20.45340.34620.15920.5723-0.27950.5788-0.03760.0411-0.1525-0.03250.0367-0.1525-0.01130.010.00090.03640.0360.01070.053-0.00820.109934.3356-27.364441.9857
30.07180.07660.2993.6689-2.08392.9940.0262-0.0538-0.0127-0.76410.0196-0.06840.603-0.2006-0.04590.2289-0.0523-0.02530.08510.00320.036616.0233-46.163463.6646
40.31050.15360.07150.3684-0.09670.12520.0311-0.0063-0.03970.0438-0.0437-0.05730.0018-0.03180.01260.06860.0086-0.02370.0654-0.00170.044221.5448-24.243348.9494
50.4135-0.054-0.04880.6153-0.05790.0133-0.00450.0183-0.0062-0.0019-0.004-0.05980.0055-0.00240.00840.03230.0077-0.00440.0883-0.01190.061729.573-2.145838.5886
62.97694.4068-2.46929.0625-6.44365.11350.1167-0.1010.3481-0.05770.02310.39750.1453-0.0648-0.13980.06560.01220.00280.1047-0.02590.05294.2732-14.793350.6512
70.57540.00810.36720.00670.00250.33450.0412-0.0375-0.10070.0034-0.00810.0210.03930.0156-0.03310.0817-0.01040.00610.0259-0.00450.1101-10.1262-42.682934.6089
81.9682-1.32190.39851.8413-1.31251.3125-0.0857-0.16530.1059-0.09610.0306-0.06430.09730.030.05510.06970.0147-0.02370.0825-0.04060.03216.5136-41.5258.6089
90.29890.08570.06230.28920.21390.1599-0.02710.0276-0.0507-0.03320.02140.0145-0.02870.02260.00570.0864-0.0005-0.01040.0622-0.01860.0357-2.1533-32.19427.5402
100.4386-0.402-0.14690.72110.11870.0518-0.03160.0147-0.08140.03430.01540.08980.00890.00230.01620.0459-0.0091-0.00690.0688-0.00650.0738-22.0585-19.978638.025
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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