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- PDB-4yng: Twinned pyruvate kinase from E. coli in the T-state -

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Basic information

Entry
Database: PDB / ID: 4yng
TitleTwinned pyruvate kinase from E. coli in the T-state
ComponentsPyruvate kinase I
KeywordsTRANSFERASE / allostery / T-state / tetramer
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / magnesium ion binding / ATP binding
Similarity search - Function
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, 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsDonovan, K.A. / Dobson, R.C.J.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Royal Society Marsden FundUOC1013 New Zealand
US Army Research LaboratoryW911NF-11-1-0481 New Zealand
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Grappling with anisotropic data, pseudo-merohedral twinning and pseudo-translational noncrystallographic symmetry: a case study involving pyruvate kinase.
Authors: Donovan, K.A. / Atkinson, S.C. / Kessans, S.A. / Peng, F. / Cooper, T.F. / Griffin, M.D. / Jameson, G.B. / Dobson, R.C.
History
DepositionMar 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Experimental preparation
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 I
B: Pyruvate kinase I
C: Pyruvate kinase I
D: Pyruvate kinase I
E: Pyruvate kinase I
F: Pyruvate kinase I
G: Pyruvate kinase I
H: Pyruvate kinase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,49120
Polymers406,3398
Non-polymers1,15312
Water44,3352461
1
A: Pyruvate kinase I
B: Pyruvate kinase I
C: Pyruvate kinase I
D: Pyruvate kinase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,74610
Polymers203,1694
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-149 kcal/mol
Surface area69680 Å2
MethodPISA
2
E: Pyruvate kinase I
F: Pyruvate kinase I
G: Pyruvate kinase I
H: Pyruvate kinase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,74610
Polymers203,1694
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-135 kcal/mol
Surface area69500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.090, 74.596, 241.634
Angle α, β, γ (deg.)90.000, 90.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 470 / Label seq-ID: 1 - 470

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF
7chain GGG
8chain HHH

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Components

#1: Protein
Pyruvate kinase I / PK-1


Mass: 50792.324 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pykF, Z2704, ECs2383 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AD62, pyruvate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2461 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 16% w/v PEG8000, 10 mM magnesium sulfate, 10 mM potassium chloride, 100 mM MES/NaOH, 0.02% w/v sodium azide
PH range: 6.2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 2, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.48
ReflectionResolution: 2.28→44.32 Å / Num. obs: 201780 / % possible obs: 95.2 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.06 / Net I/σ(I): 9.7 / Num. measured all: 671834 / Scaling rejects: 428
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.28-2.322.50.3332186888960.8120.25685.6
12.49-44.323.30.03517.2435813270.9970.02295.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
REFMACrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→44.131 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 2253 1.12 %Thin shells
Rwork0.2166 186404 --
obs0.2194 201704 95.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.03 Å2 / Biso mean: 31.4105 Å2 / Biso min: 9.73 Å2
Refinement stepCycle: final / Resolution: 2.28→44.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27957 0 60 2461 30478
Biso mean--32.17 26.63 -
Num. residues----3720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328317
X-RAY DIFFRACTIONf_angle_d0.80238206
X-RAY DIFFRACTIONf_chiral_restr0.0324610
X-RAY DIFFRACTIONf_plane_restr0.0034933
X-RAY DIFFRACTIONf_dihedral_angle_d10.93810645
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A21319X-RAY DIFFRACTION12.743TORSIONAL
12B21319X-RAY DIFFRACTION12.743TORSIONAL
13C21319X-RAY DIFFRACTION12.743TORSIONAL
14D21319X-RAY DIFFRACTION12.743TORSIONAL
15E21319X-RAY DIFFRACTION12.743TORSIONAL
16F21319X-RAY DIFFRACTION12.743TORSIONAL
17G21319X-RAY DIFFRACTION12.743TORSIONAL
18H21319X-RAY DIFFRACTION12.743TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3143-2.36670.29332280.2673115881181689
2.3667-2.42420.33121200.2633121221224293
2.4242-2.48770.27481170.2535123981251594
2.4877-2.55850.27191210.2537124541257595
2.5585-2.63810.29331220.251125191264196
2.6381-2.72860.26171190.2473124841260395
2.7286-2.83290.23871250.2347126921281797
2.8329-2.95530.30441300.2354127021283297
2.9553-3.1020.2682440.2249126321287696
3.102-3.2830.20771200.2281127041282497
3.283-3.51530.28521140.2212124081252294
3.5153-3.83150.21431060.2105121451225192
3.8315-4.30470.23471220.1879120221214491
4.3047-5.15610.20331180.1645125831270195
5.1561-7.86680.20192440.202129511319597

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