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- PDB-4krz: Apo crystal structure of pyruvate kinase (PYK) from Trypanosoma cruzi -

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Basic information

Entry
Database: PDB / ID: 4krz
TitleApo crystal structure of pyruvate kinase (PYK) from Trypanosoma cruzi
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
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhong, W. / Morgan, H.P. / 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 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)113,9566
Polymers113,6942
Non-polymers2624
Water8,125451
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,91312
Polymers227,3884
Non-polymers5258
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14910 Å2
ΔGint-69 kcal/mol
Surface area73750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.785, 121.415, 97.160
Angle α, β, γ (deg.)90.00, 115.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
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: I04 / Wavelength: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→43.77 Å / Num. obs: 38483 / % possible obs: 93.7 % / Observed criterion σ(I): 13.7
Reflection shellResolution: 2.5→2.64 Å / % possible all: 90.5

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QV9

3qv9


Resolution: 2.5→41.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.905 / SU B: 13.622 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.577 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22285 1932 5 %RANDOM
Rwork0.16056 ---
obs0.16365 36536 93.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.402 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.06 Å2
2--0.09 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7564 0 14 451 8029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197742
X-RAY DIFFRACTIONr_angle_refined_deg1.0271.9710473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98151003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50524.428332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.815151393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8621554
X-RAY DIFFRACTIONr_chiral_restr0.0810.21213
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215768
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 131 -
Rwork0.204 2472 -
obs--87.12 %
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)
13.027-2.99742.75993.0142-3.11385.79140.0132-0.0350.0160.06790.0503-0.0147-0.47140.0031-0.06350.20190.0144-0.00340.09670.0090.188618.652940.868335.2247
20.34090.0096-0.47540.30530.19650.81590.05710.16050.03870.02060.0675-0.0556-0.0708-0.1893-0.12460.1269-0.0195-0.02810.2490.02710.117811.458823.66186.0118
33.44562.3320.15981.5910.05221.47430.04640.16740.69910.05380.09080.48850.30950.1602-0.13710.1819-0.022-0.04510.05210.03880.3205-8.56-2.26822.087
40.5315-0.2102-0.00170.21910.15760.56710.03460.0963-0.05120.0440.0287-0.01870.0058-0.0579-0.06330.1412-0.0206-0.01390.1615-0.01070.158712.259716.745519.2598
51.08590.08610.23240.01280.00311.0572-0.03920.1138-0.00770.01420.01740.01970.00320.04120.02190.1513-0.02630.0140.1711-0.00580.125234.631528.439915.7874
67.09564.9747-1.65364.88680.1361.5917-0.4390.1904-0.244-0.16110.3597-0.14720.25760.12130.07930.1752-0.01120.02180.15540.06320.154818.576614.809338.2073
70.2692-0.2145-0.3550.23410.14811.3339-0.03510.0966-0.01110.04120.0344-0.00770.0545-0.34720.00060.07570.05230.01660.28990.04190.1327-8.700430.117452.9264
81.50580.3692-0.09890.3327-0.04280.9638-0.00270.0775-0.16210.12950.08270.0175-0.08090.0456-0.080.2424-0.0148-0.03050.04240.05070.1986-10.745755.560725.6773
90.0949-0.0725-0.10740.3961-0.14460.87720.00480.0574-0.03180.00750.0698-0.0643-0.1753-0.2132-0.07470.1720.07610.01260.1710.02350.14320.682137.648743.9676
101.30830.068-0.37010.0596-0.17620.56720.0181-0.08370.06870.00050.023-0.0056-0.0225-0.027-0.04110.15920.02270.00170.1631-0.01230.146214.907927.877662.6201
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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