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- PDB-6qxl: Crystal Structure of Pyruvate Kinase II (PykA) from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 6qxl
TitleCrystal Structure of Pyruvate Kinase II (PykA) from Pseudomonas aeruginosa in complex with sodium malonate, magnesium and glucose-6-phosphate
ComponentsPyruvate kinase
KeywordsTRANSFERASE / Pyruvate kinase / PykA / homotetramer / polypeptide / G6P-bound / PykA-MLI-Mg complex
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / magnesium ion binding / ATP binding / cytosol / 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 / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / MALONATE ION / Pyruvate kinase / Pyruvate kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.43 Å
AuthorsAbdelhamid, Y. / Brear, P. / Welch, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Yousef Jameel Scholarship United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Evolutionary plasticity in the allosteric regulator-binding site of pyruvate kinase isoform PykA fromPseudomonas aeruginosa.
Authors: Abdelhamid, Y. / Brear, P. / Greenhalgh, J. / Chee, X. / Rahman, T. / Welch, M.
History
DepositionMar 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jul 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_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.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.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 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
D: Pyruvate kinase
E: Pyruvate kinase
F: Pyruvate kinase
G: Pyruvate kinase
H: Pyruvate kinase
I: Pyruvate kinase
J: Pyruvate kinase
K: Pyruvate kinase
L: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)632,82551
Polymers627,91112
Non-polymers4,91439
Water40,8582268
1
A: Pyruvate kinase
E: Pyruvate kinase
G: Pyruvate kinase
H: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,94217
Polymers209,3044
Non-polymers1,63813
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pyruvate kinase
D: Pyruvate kinase
F: Pyruvate kinase
J: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,03418
Polymers209,3044
Non-polymers1,73014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pyruvate kinase
I: Pyruvate kinase
K: Pyruvate kinase
L: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,85016
Polymers209,3044
Non-polymers1,54612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.477, 182.477, 405.044
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 24 molecules ABCDEFGHIJKL

#1: Protein
Pyruvate kinase


Mass: 52325.930 Da / Num. of mol.: 12 / Fragment: Polypeptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pykA, pyk, pykA_1, C8257_26620, CAZ10_21690, DZ940_08845, NCTC13719_04679, PAERUG_E15_London_28_01_14_03018, PAMH19_3832, RW109_RW109_05666
Plasmid: pET19m / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A069PYA5, UniProt: Q9HW72*PLUS, pyruvate kinase
#2: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 2295 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2268 / 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: 3.1 Å3/Da / Density % sol: 60.33 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 % PEG 3350, 0.1 M Bis-Tris propane pH 7.5, 0.2 M disodium malonate, 20 mM MgCl2, 2 mM G6P and 2 mM PEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.43→405.44 Å / Num. obs: 292996 / % possible obs: 100 % / Redundancy: 14.7 % / Biso Wilson estimate: 45.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.038 / Rrim(I) all: 0.148 / Net I/σ(I): 11.1 / Num. measured all: 4318494 / Scaling rejects: 4029
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.43-2.4910.52.21226510214770.6420.712.3241.1
10.87-405.4414.90.03353910361710.0090.03438

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HYV

4hyv


Resolution: 2.43→158.03 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.37 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.243
RfactorNum. reflection% reflectionSelection details
Rfree0.251 14331 4.95 %RANDOM
Rwork0.227 ---
obs0.228 289310 98.9 %-
Displacement parametersBiso max: 235.94 Å2 / Biso mean: 55.44 Å2 / Biso min: 19.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.2314 Å20 Å20 Å2
2--0.2314 Å20 Å2
3----0.4629 Å2
Refinement stepCycle: final / Resolution: 2.43→158.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43331 0 306 2268 45905
Biso mean--62.51 50.59 -
Num. residues----5716
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d15855SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes1026HARMONIC2
X-RAY DIFFRACTIONt_gen_planes6547HARMONIC5
X-RAY DIFFRACTIONt_it44269HARMONIC20
X-RAY DIFFRACTIONt_nbd10SEMIHARMONIC0
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion5949SEMIHARMONIC5
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_contact51243SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d44269HARMONIC20.014
X-RAY DIFFRACTIONt_angle_deg59874HARMONIC21.62
X-RAY DIFFRACTIONt_omega_torsion5.07
X-RAY DIFFRACTIONt_other_torsion16.8
LS refinement shellResolution: 2.43→2.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3146 1071 5.05 %
Rwork0.2967 20138 -
all0.2976 21209 -
obs--98.88 %

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