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- PDB-3hqo: Crystal structures of Leishmania mexicana pyruvate kinase (LmPYK)... -

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Basic information

Entry
Database: PDB / ID: 3hqo
TitleCrystal structures of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP and Oxalate
ComponentsPyruvate kinase
KeywordsTRANSFERASE / TIM BARREL / R-STATE ENZYME / Allosteric enzyme / Glycolysis / Kinase / Magnesium / Metal-binding / Pyruvate
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / magnesium ion binding / ATP binding
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
ADENOSINE-5'-TRIPHOSPHATE / : / OXALATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsMorgan, H.P. / Walkinshaw, M.D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The allosteric mechanism of pryuvate kinase from Leishmania mexicana: a rock and lock model
Authors: Morgan, H.P. / McNae, I.W. / Nowicki, M.W. / Hannaert, V. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
History
DepositionJun 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ncs_dom_lim / 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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
K: Pyruvate kinase
A: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,55522
Polymers217,8724
Non-polymers2,68318
Water00
1
K: Pyruvate kinase
hetero molecules

K: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,30212
Polymers108,9362
Non-polymers1,36610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5220 Å2
ΔGint-48 kcal/mol
Surface area40930 Å2
MethodPISA
2
A: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,30212
Polymers108,9362
Non-polymers1,36610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area5200 Å2
ΔGint-48 kcal/mol
Surface area40960 Å2
MethodPISA
3
B: Pyruvate kinase
hetero molecules

B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,25310
Polymers108,9362
Non-polymers1,3178
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4840 Å2
ΔGint-24 kcal/mol
Surface area41420 Å2
MethodPISA
4
C: Pyruvate kinase
hetero molecules

C: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,25310
Polymers108,9362
Non-polymers1,3178
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area4840 Å2
ΔGint-24 kcal/mol
Surface area41700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.516, 128.133, 204.361
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11K
21A
31B
41C

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYS2KA1 - 852 - 86
21LYSLYS2AB1 - 852 - 86
31LYSLYS2BC1 - 852 - 86
41LYSLYS2CD1 - 852 - 86
12GLUGLU1KA190 - 498191 - 499
22GLUGLU1AB190 - 498191 - 499
32GLUGLU1BC190 - 498191 - 499
42GLUGLU1CD190 - 498191 - 499

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Components

#1: Protein
Pyruvate kinase / PK


Mass: 54467.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Strain: NHOM/B2/84/BEL46 / Gene: PYK / Plasmid: pET3A_lmPYK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q27686, pyruvate kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Sequence detailsTHE SEQUENCE OF L. MEXICANA PYRUVATE KINASE HAS BEEN DETERMINED IN THE LABORATORY OF PROF. PAUL ...THE SEQUENCE OF L. MEXICANA PYRUVATE KINASE HAS BEEN DETERMINED IN THE LABORATORY OF PROF. PAUL MICHELS, PUBLISHED AND DEPOSITED IN GENBANK. HOWEVER, THE SEQUENCE AS APPEARED IN GENBANK CONTAINED ERRORS. THE CORRECTION HAS BEEN INFORMED TO GENBANK WITH THE ACCESSION CODE X74944 AND IT WILL BE FILTRATED TO UNIPROT AT A LATER TIME.

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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: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 10-16% PEG8000, 20mM triethanolamine-HCl, 50mM MgCl2, 100mM KCl, 10-15% glycerol, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 8, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.4→82.48 Å / Num. all: 106471 / Num. obs: 36748 / % possible obs: 96.2 % / Observed criterion σ(F): 3.4 / Observed criterion σ(I): 3.4 / Redundancy: 2.9 % / Biso Wilson estimate: 54.14 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 6.5
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5452 / % possible all: 98.5

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.2.0019refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PKL

1pkl


Resolution: 3.4→41.18 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.845 / SU B: 70.964 / SU ML: 0.516 / Cross valid method: THROUGHOUT / ESU R Free: 0.67 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28951 1831 5 %RANDOM
Rwork0.25052 ---
obs0.25243 34917 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.828 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20.64 Å2
2--8.06 Å20 Å2
3----6.95 Å2
Refinement stepCycle: LAST / Resolution: 3.4→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14988 0 158 0 15146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02215440
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.96420936
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75651972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33524.826688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.352152652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9261596
X-RAY DIFFRACTIONr_chiral_restr0.0670.22420
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211572
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.26736
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.210677
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.2151
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1511.59784
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.377215824
X-RAY DIFFRACTIONr_scbond_it3.68735724
X-RAY DIFFRACTIONr_scangle_it6.8224.55112
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1K2655tight positional0.020.05
2A2655tight positional0.020.05
3B2655tight positional0.020.05
4C2655tight positional0.020.05
1K300medium positional0.220.5
2A300medium positional0.250.5
3B300medium positional0.220.5
4C300medium positional0.270.5
1K2655tight thermal0.020.5
2A2655tight thermal0.020.5
3B2655tight thermal0.020.5
4C2655tight thermal0.020.5
1K300medium thermal0.162
2A300medium thermal0.172
3B300medium thermal0.152
4C300medium thermal0.172
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 150 -
Rwork0.351 2625 -
obs--98.44 %

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