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- PDB-6ksh: Crystal structure of pyruvate kinase (PYK) from Plasmodium falcip... -

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Basic information

Entry
Database: PDB / ID: 6ksh
TitleCrystal structure of pyruvate kinase (PYK) from Plasmodium falciparum in complex with oxalate and ATP
ComponentsPyruvate kinase
KeywordsTRANSFERASE / pyruvate kinase / glycolysis / tetramer / allostery
Function / homology
Function and homology information


Glycolysis / Neutrophil degranulation / pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / protein homotetramerization / phosphorylation / magnesium ion binding ...Glycolysis / Neutrophil degranulation / pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / protein homotetramerization / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
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 ...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 / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / OXALATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhong, W. / Cai, Q. / Li, K. / Lescar, J. / Dedon, P.C.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (Singapore)S916137 Singapore
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Pyruvate kinase from Plasmodium falciparum: Structural and kinetic insights into the allosteric mechanism.
Authors: Zhong, W. / Li, K. / Cai, Q. / Guo, J. / Yuan, M. / Wong, Y.H. / Walkinshaw, M.D. / Fothergill-Gilmore, L.A. / Michels, P.A.M. / Dedon, P.C. / Lescar, J.
History
DepositionAug 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
D: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,66424
Polymers223,9324
Non-polymers2,73220
Water17,114950
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15310 Å2
ΔGint-79 kcal/mol
Surface area70080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.410, 139.410, 453.156
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pyruvate kinase /


Mass: 55983.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0626800 / Plasmid: pYUB28b-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C6KTA4, pyruvate kinase

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Non-polymers , 5 types, 970 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 950 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 12% PEG 8000, 20% glycerol, 50 mM triethanolamine-HCl (TEA) buffer pH 7.2, 100 mM KCl, 50 mM MgCl2, 5 mM oxalate, 5 mM ATP, 5 mM G6P

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→120.733 Å / Num. all: 81169 / Num. obs: 81169 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 58.38 Å2 / Rpim(I) all: 0.042 / Rrim(I) all: 0.194 / Rsym value: 0.19 / Net I/av σ(I): 3.8 / Net I/σ(I): 15.4 / Num. measured all: 1695738
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.6-2.7421.61.3190.6251897116400.2881.351.3193.1100
2.74-2.9121.50.8630.9237650110280.1890.8830.8634.5100
2.91-3.1121.50.5181.4222385103570.1140.5310.5187100
3.11-3.3621.30.332.320639996870.0730.3380.3310.4100
3.36-3.6821.10.1943.818949789800.0430.1990.19416.4100
3.68-4.1120.80.1285.716973581500.0290.1310.12823.1100
4.11-4.7520.50.1016.814852072510.0230.1040.10130.1100
4.75-5.8119.30.1026.512000262240.0240.1050.10228.3100
5.81-8.2218.90.0778.39321649200.0180.0790.07727.8100
8.22-59.83819.20.05111.85643729320.0120.0520.05142.299.7

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KHD

3khd


Resolution: 2.6→37.99 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.473 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.207 4015 4.96 %RANDOM
Rwork0.151 ---
obs0.154 81001 100 %-
Displacement parametersBiso max: 149.93 Å2 / Biso mean: 55.14 Å2 / Biso min: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.3365 Å20 Å20 Å2
2---2.3365 Å20 Å2
3---4.673 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2.6→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14932 0 160 950 16042
Biso mean--50.96 54.09 -
Num. residues----1960
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5593SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2610HARMONIC5
X-RAY DIFFRACTIONt_it15323HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2178SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18520SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d15323HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg20721HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion19.87
LS refinement shellResolution: 2.6→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2722 90 5.55 %
Rwork0.2024 1531 -
all0.2063 1621 -
obs--100 %
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)
1-3.91390.9583-6.09748.42221.72910-0.0183-0.28740.57890.32970.04240.4233-0.438-0.3024-0.024-0.12570.13880.0112-0.133-0.1551-0.048419.6265-15.9233-20.2339
22.77640.0993-0.18090.73020.00340.9782-0.0383-0.54780.18560.2577-0.07950.052-0.0201-0.10930.1179-0.0789-0.0562-0.00580.1093-0.1784-0.152939.8024-29.92320.9287
31.9033-0.07340.40262.6946-1.04153.4398-0.01340.0072-0.0218-0.0629-0.07-0.5280.10660.74390.0834-0.16050.0189-0.03060.0752-0.0891-0.075663.3315-33.6471-12.6072
41.66810.26560.15791.02640.10031.37890.0049-0.2332-0.10340.0556-0.047-0.03750.2088-0.09560.0421-0.0351-0.05010.005-0.011-0.0902-0.126436.0971-37.8486-13.2323
55.17650.25651.80442.25990.35262.35880.1286-1.05110.42890.0515-0.2070.2284-0.2448-0.32390.0784-0.161-0.12470.08720.1237-0.2058-0.155115.1189-38.1961-2.7695
67.4509-7.11323.08832.28815.082.76290.14050.55590.0372-0.7578-0.1378-0.35920.42930.3412-0.00270.07760.04720.09610.0754-0.1039-0.043443.8829-43.219-32.7036
71.93230.6092-0.25230.82090.29651.6738-0.12520.25850.3958-0.40530.0679-0.3434-0.44350.31720.05730.0587-0.1510.0057-0.1529-0.0263-0.113249.2411-12.4438-41.0443
81.30110.17210.9811.79670.3413.9127-0.1155-0.22670.6225-0.02020.11770.1156-0.8079-0.0628-0.00220.0652-0.038-0.0169-0.2856-0.20770.105242.62852.3876-18.963
90.8158-0.00380.36311.44930.05812.0873-0.12290.01940.3085-0.2060.04660.1242-0.3796-0.1880.07630.0206-0.0279-0.0468-0.137-0.0642-0.073533.899-17.1113-36.425
104.28680.8508-1.32694.90680.37023.4253-0.19030.33-0.185-0.71480.1996-0.2247-0.23990.1964-0.00930.1097-0.11570.0124-0.1048-0.0634-0.224335.7027-29.5219-56.3634
11-3.61392.03024.90143.80880.70373.0615-0.14-0.0643-0.37450.4095-0.12270.00930.35370.11620.2627-0.09680.0134-0.019-0.0547-0.0668-0.12895.8227-68.6165-36.1755
12-0.57240.2913-0.26572.1-0.02462.1658-0.0179-0.10630.08360.06-0.09750.6006-0.0224-0.60760.1154-0.1744-0.00030.01150.0842-0.1797-0.0623-24.6363-60.7537-28.5552
134.9017-1.0836-1.12661.6130.22595.68360.18570.69330.2764-0.5008-0.19030.6302-0.6045-1.04050.0047-0.2750.1577-0.18720.0174-0.1208-0.0236-35.2594-49.4231-51.1508
141.1664-0.2056-0.16541.05060.20391.9888-0.0141-0.02470.285-0.104-0.09390.2136-0.447-0.27420.108-0.07030.0464-0.0364-0.031-0.1535-0.0487-14.3118-48.7197-33.5834
153.126-0.5606-0.32482.3686-0.75632.2962-0.0002-0.27730.0150.1489-0.08230.0671-0.1119-0.32490.0825-0.0895-0.0407-0.02380.0423-0.1962-0.1317-4.2399-54.1606-12.8306
162.3551-0.92572.53212.7099-1.35520.00070.18820.21580.3677-0.2953-0.2504-0.0285-0.1702-0.15560.06220.19230.0621-0.1076-0.139-0.07870.0431-9.4184-35.6986-50.1723
171.12430.9563-0.26671.9302-0.10811.179-0.14130.2380.1813-0.31540.06340.1178-0.3366-0.11260.07790.0582-0.0859-0.0848-0.0673-0.0206-0.1465-3.8663-60.4799-70.1675
182.37220.2243-0.32651.7466-0.01812.5066-0.0643-0.1527-0.1626-0.1133-0.05880.13810.151-0.15410.12310.0139-0.0667-0.0041-0.0106-0.1129-0.06-10.0306-83.1562-56.0626
190.69080.31410.01131.160.08831.0416-0.122-0.02790.0521-0.1433-0.008-0.0685-0.19340.06140.130.0012-0.0587-0.0179-0.0287-0.0541-0.10084.5035-59.7228-55.8027
202.08190.94570.60954.72011.40444.0847-0.29710.18870.2868-0.59860.14060.0333-0.5636-0.2210.15650.0783-0.1164-0.0334-0.17160.0314-0.139613.6125-40.9528-66.7219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|21 - A|31 }A21 - 31
2X-RAY DIFFRACTION2{ A|32 - A|113 }A32 - 113
3X-RAY DIFFRACTION3{ A|114 - A|213 }A114 - 213
4X-RAY DIFFRACTION4{ A|214 - A|395 }A214 - 395
5X-RAY DIFFRACTION5{ A|396 - A|511 }A396 - 511
6X-RAY DIFFRACTION6{ B|21 - B|31 }B21 - 31
7X-RAY DIFFRACTION7{ B|32 - B|113 }B32 - 113
8X-RAY DIFFRACTION8{ B|114 - B|213 }B114 - 213
9X-RAY DIFFRACTION9{ B|214 - B|395 }B214 - 395
10X-RAY DIFFRACTION10{ B|396 - B|511 }B396 - 511
11X-RAY DIFFRACTION11{ C|21 - C|31 }C21 - 31
12X-RAY DIFFRACTION12{ C|32 - C|113 }C32 - 113
13X-RAY DIFFRACTION13{ C|114 - C|213 }C114 - 213
14X-RAY DIFFRACTION14{ C|214 - C|395 }C214 - 395
15X-RAY DIFFRACTION15{ C|396 - C|511 }C396 - 511
16X-RAY DIFFRACTION16{ D|21 - D|31 }D21 - 31
17X-RAY DIFFRACTION17{ D|32 - D|113 }D32 - 113
18X-RAY DIFFRACTION18{ D|114 - D|213 }D114 - 213
19X-RAY DIFFRACTION19{ D|214 - D|395 }D214 - 395
20X-RAY DIFFRACTION20{ D|396 - D|511 }D396 - 511

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