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- PDB-5ws8: Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex ... -

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Basic information

Entry
Database: PDB / ID: 5ws8
TitlePyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate
ComponentsPyruvate kinase
KeywordsTRANSFERASE / pyruvate kinase / glycolysis / tetramer / allostery / synergism / phospho transferase
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / magnesium ion binding / ATP binding / plasma membrane / cytoplasm / cytosol
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
OXALATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsZhong, W. / Cai, Q. / El Sahili, A. / Lescar, J. / Dedon, P.C.
Funding support Singapore, 2items
OrganizationGrant numberCountry
National Research Foundation funding through SMARTS916137 Singapore
Singapore-MIT Alliance for Research and Technology (SMART) FellowshipS900184 Singapore
CitationJournal: Nat Commun / Year: 2017
Title: Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis.
Authors: Zhong, W. / Cui, L. / Goh, B.C. / Cai, Q. / Ho, P. / Chionh, Y.H. / Yuan, M. / Sahili, A.E. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. / Lescar, J. / Dedon, P.C.
History
DepositionDec 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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
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_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 / _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

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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)204,50712
Polymers204,0574
Non-polymers4498
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-76 kcal/mol
Surface area68540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.011, 127.011, 144.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 2 - 472 / Label seq-ID: 5 - 475

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
6
1
2
3
4
5

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Components

#1: Protein
Pyruvate kinase / PK


Mass: 51014.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pyk, pykA, Rv1617, MTCY01B2.09 / Plasmid: pYUB28b-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WKE5, pyruvate kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 3.32 Å3/Da / Density % sol: 63.44 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.62→63.51 Å / Num. obs: 78513 / % possible obs: 100 % / Redundancy: 5.5 % / Net I/σ(I): 10.6
Reflection shellResolution: 2.62→2.67 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WRP

5wrp


Resolution: 2.62→63.51 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 22.036 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.439 / ESU R Free: 0.257 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21784 4011 5.1 %RANDOM
Rwork0.1734 ---
obs0.17562 74461 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.639 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20.9 Å20 Å2
2--1.81 Å20 Å2
3----5.87 Å2
Refinement stepCycle: 1 / Resolution: 2.62→63.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14008 0 28 494 14530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914256
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213864
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.97419352
X-RAY DIFFRACTIONr_angle_other_deg0.651331924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44651856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17723.289596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.867152448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.03415148
X-RAY DIFFRACTIONr_chiral_restr0.0720.22320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022768
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0944.1337436
X-RAY DIFFRACTIONr_mcbond_other3.0914.1317435
X-RAY DIFFRACTIONr_mcangle_it4.8266.1929288
X-RAY DIFFRACTIONr_mcangle_other4.8266.1949289
X-RAY DIFFRACTIONr_scbond_it3.674.5256820
X-RAY DIFFRACTIONr_scbond_other3.6514.526801
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6646.61810041
X-RAY DIFFRACTIONr_long_range_B_refined9.49779.50559645
X-RAY DIFFRACTIONr_long_range_B_other9.47979.39659350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A292100.06
12B292100.06
21A290440.08
22C290440.08
31A290160.07
32D290160.07
41B291340.07
42C291340.07
51B291580.07
52D291580.07
61C290660.07
62D290660.07
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 302 -
Rwork0.307 5575 -
obs--99.93 %
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)
13.35232.2412-1.09725.2417-0.36712.9967-0.15050.17920.0739-0.28770.10830.39670.007-0.56060.04220.1169-0.1002-0.05320.22660.03990.050124.8154-2.8249-31.9548
22.2219-0.14740.47763.39332.98478.6132-0.06010.0204-0.3332-0.1131-0.09880.40140.3668-0.9680.15890.3252-0.04660.01550.42420.07880.26414.2911-24.779-9.6594
31.61290.02780.25672.53140.44593.5076-0.17070.1279-0.1961-0.09450.1973-0.07810.34860.2182-0.02660.0798-0.0460.00620.18220.04440.054432.9794-9.7506-20.6548
48.04711.13230.4580.62850.73783.19590.00850.38520.0191-0.29840.1428-0.1779-0.02950.3276-0.15120.3067-0.09530.07890.36040.03360.153351.35871.4085-35.4181
53.7852-2.8660.91625.4012-0.64943.0904-0.1291-0.1853-0.14660.24030.1140.4171-0.0112-0.52910.01510.11710.09930.04920.20430.03240.046624.80742.824216.7272
62.19320.0474-0.85133.273.0968.4135-0.0067-0.050.35460.1199-0.13780.3987-0.3176-1.00920.14440.3340.0581-0.01760.42330.08580.281614.299124.7813-5.5704
71.6189-0.1102-0.11192.56490.50643.3372-0.1712-0.09980.20850.09530.212-0.0516-0.35530.2038-0.04080.07660.0375-0.00650.17590.03750.047832.989.7585.4383
87.9283-0.9346-0.52720.8820.57333.3006-0.0046-0.4088-0.07390.38330.0918-0.1803-0.03150.3682-0.08710.26370.0939-0.05040.3790.04370.127651.3993-1.376420.2112
94.02862.84811.18885.53430.60643.2082-0.14960.1572-0.1263-0.33760.0789-0.45840.04830.61230.07070.1268-0.09790.06070.2337-0.01620.0534102.20342.8224-31.9517
102.3373-0.4401-0.32433.5918-3.38758.9101-0.01130.04270.3037-0.1399-0.1456-0.3978-0.35991.03410.15680.3179-0.0649-0.0020.4352-0.08840.2689112.705124.7717-9.6919
111.64410.1343-0.2832.5326-0.51993.7949-0.17920.10060.2074-0.11040.20630.0678-0.3529-0.1894-0.02710.0779-0.0428-0.01110.1728-0.0420.050394.0099.7503-20.656
128.09891.3759-0.4950.6173-0.74653.23090.00440.3505-0.0438-0.28080.12910.1274-0.0244-0.3366-0.13350.3568-0.0717-0.08170.3701-0.04980.151375.6402-1.3533-35.4154
133.301-2.3058-0.89964.85150.79683.7427-0.1914-0.22070.10350.31920.1684-0.3595-0.05740.56010.0230.1270.1087-0.05780.2197-0.03950.0426102.1968-2.827416.7379
141.46220.57710.56043.7003-3.34118.7037-0.0042-0.0341-0.33610.0702-0.1207-0.42190.31390.90320.12490.30030.04910.02820.4088-0.08830.2939112.6871-24.7733-5.5339
151.704-0.06530.26562.3708-0.55933.4778-0.175-0.0987-0.19130.08250.21630.07850.3706-0.1856-0.04130.08210.03940.00680.1772-0.04480.049694.0122-9.7555.4343
167.7088-1.18270.35280.9281-0.68953.3381-0.0204-0.4607-0.00260.34910.12770.19760.0322-0.3779-0.10720.25330.10590.0450.3836-0.05270.14175.6341.354720.2161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 70
2X-RAY DIFFRACTION2A71 - 167
3X-RAY DIFFRACTION3A168 - 344
4X-RAY DIFFRACTION4A345 - 467
5X-RAY DIFFRACTION5B2 - 70
6X-RAY DIFFRACTION6B71 - 167
7X-RAY DIFFRACTION7B168 - 344
8X-RAY DIFFRACTION8B345 - 467
9X-RAY DIFFRACTION9C2 - 70
10X-RAY DIFFRACTION10C71 - 167
11X-RAY DIFFRACTION11C168 - 344
12X-RAY DIFFRACTION12C345 - 467
13X-RAY DIFFRACTION13D2 - 70
14X-RAY DIFFRACTION14D71 - 167
15X-RAY DIFFRACTION15D168 - 344
16X-RAY DIFFRACTION16D345 - 467

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