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- PDB-1pkl: THE STRUCTURE OF LEISHMANIA PYRUVATE KINASE -

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Basic information

Entry
Database: PDB / ID: 1pkl
TitleTHE STRUCTURE OF LEISHMANIA PYRUVATE KINASE
ComponentsPROTEIN (PYRUVATE KINASE)
KeywordsTRANSFERASE / PYRUVATE KINASE / GLYCOLYTIC ENZYME / HOMOTETRAMER
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
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / 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 ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / 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 / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.35 Å
AuthorsRigden, D.J. / Phillips, S.E.V. / Michels, P.A.M. / Fothergill-Gilmore, L.A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: The structure of pyruvate kinase from Leishmania mexicana reveals details of the allosteric transition and unusual effector specificity.
Authors: Rigden, D.J. / Phillips, S.E. / Michels, P.A. / Fothergill-Gilmore, L.A.
History
DepositionSep 15, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 23, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: PROTEIN (PYRUVATE KINASE)
B: PROTEIN (PYRUVATE KINASE)
C: PROTEIN (PYRUVATE KINASE)
D: PROTEIN (PYRUVATE KINASE)
E: PROTEIN (PYRUVATE KINASE)
F: PROTEIN (PYRUVATE KINASE)
H: PROTEIN (PYRUVATE KINASE)
G: PROTEIN (PYRUVATE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)436,51216
Polymers435,7438
Non-polymers7698
Water53,1802952
1
A: PROTEIN (PYRUVATE KINASE)
B: PROTEIN (PYRUVATE KINASE)
C: PROTEIN (PYRUVATE KINASE)
D: PROTEIN (PYRUVATE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,2568
Polymers217,8724
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13440 Å2
ΔGint-152 kcal/mol
Surface area75600 Å2
MethodPISA, PQS
2
E: PROTEIN (PYRUVATE KINASE)
F: PROTEIN (PYRUVATE KINASE)
H: PROTEIN (PYRUVATE KINASE)
G: PROTEIN (PYRUVATE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,2568
Polymers217,8724
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13430 Å2
ΔGint-152 kcal/mol
Surface area75840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.649, 132.638, 180.996
Angle α, β, γ (deg.)90.00, 97.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN (PYRUVATE KINASE)


Mass: 54467.934 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Strain: MHOM/BZ/84/BEL46 / Cellular location: CYTOSOL / Gene: PYK / Plasmid: PET3A / Cellular location (production host): CYTOSOL / Gene (production host): PYK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q27686, pyruvate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2952 / 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: 3.33 Å3/Da / Density % sol: 62.8 %
Crystal growpH: 4.8
Details: 6% PEG 4000, 20MM AMMONIUM SULPHATE, 15% GLYCEROL, 20MM SODIUM ACETATE PH 4.8
Crystal
*PLUS
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMsodium acetate1reservoir
220 mMammonium sulfate1reservoir
36 %(w/v)PEG40001reservoir
415 %(v/v)glycerol1reservoir
58-12 mg/mlprotain1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: BENT FUSED QUARTZ SINGLE SEGMENT MIRROR
RadiationMonochromator: 200MM LONG BENT, TRIANGULAR GE(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 160789 / % possible obs: 68 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 5.4
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.4 / % possible all: 47.4
Reflection
*PLUS
% possible obs: 68 %
Reflection shell
*PLUS
% possible obs: 47.4 %

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Processing

Software
NameVersionClassification
AMoREphasing
FFTmodel building
SHELXSphasing
MLPHAREphasing
DMmodel building
X-PLOR3.851refinement
DENZOdata reduction
CCP4(SCALA)data scaling
FFTphasing
DMphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1PKY

1pky


Resolution: 2.35→30 Å / Rfactor Rfree error: 0.0028 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 8074 5 %RANDOM
Rwork0.209 ---
obs0.209 160789 67.9 %-
Displacement parametersBiso mean: 48.9 Å2
Baniso -1Baniso -2Baniso -3
1--12.518 Å20 Å2-4.1509 Å2
2--11.1994 Å20 Å2
3---1.3186 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29994 0 40 2952 32986
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.35→2.43 Å / Rfactor Rfree error: 0.18 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.404 523 5 %
Rwork0.367 10147 -
obs--46.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.ELEMENTSTOPOLOGY.ELEMENTS
X-RAY DIFFRACTION3PARAM.SO4TOP.SO4
X-RAY DIFFRACTION4PARAM.WAT_NOHTOP.WAT_NOH
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 48.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
LS refinement shell
*PLUS
Rfactor Rfree: 0.404 / % reflection Rfree: 5 % / Rfactor Rwork: 0.367 / Rfactor obs: 0.369

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