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- PDB-6asi: E. coli phosphoenolpyruvate carboxykinase G209S mutant bound to m... -

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Basic information

Entry
Database: PDB / ID: 6asi
TitleE. coli phosphoenolpyruvate carboxykinase G209S mutant bound to methanesulfonate
ComponentsPhosphoenolpyruvate carboxykinase (ATP)Phosphoenolpyruvate carboxykinase (ATP)
KeywordsLYASE / Nonnative ligand
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / calcium ion binding / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate carboxykinase, C-terminal ...Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
methanesulfonic acid / ADENOSINE-5'-TRIPHOSPHATE / : / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.789 Å
AuthorsTang, H.Y.H. / Shin, D.S. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)ARPA-E REMOTE United States
Department of Energy (DOE, United States)Integrated Diffraction Analysis Technologies United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase.
Authors: Tang, H.Y.H. / Shin, D.S. / Hura, G.L. / Yang, Y. / Hu, X. / Lightstone, F.C. / McGee, M.D. / Padgett, H.S. / Yannone, S.M. / Tainer, J.A.
History
DepositionAug 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 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_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 1, 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 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase (ATP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2515
Polymers60,5681
Non-polymers6834
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.310, 93.312, 46.525
Angle α, β, γ (deg.)90.00, 96.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

21A-845-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoenolpyruvate carboxykinase (ATP) / Phosphoenolpyruvate carboxykinase (ATP) / PEPCK


Mass: 60568.098 Da / Num. of mol.: 1 / Mutation: G209S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pckA, pck, b3403, JW3366 / Production host: Escherichia coli (E. coli)
References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP)

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Non-polymers , 5 types, 216 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-03S / methanesulfonic acid / Methanesulfonic acid


Mass: 96.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.3 M sodium chloride, 0.1 M sodium methanesulfonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.789→46.7 Å / Num. obs: 91394 / % possible obs: 92.4 % / Redundancy: 2.23 % / Net I/σ(I): 18.39

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.789→46.656 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.31
RfactorNum. reflection% reflection
Rfree0.1851 3616 3.96 %
Rwork0.1659 --
obs0.1667 91393 92.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.789→46.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 38 212 4273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054178
X-RAY DIFFRACTIONf_angle_d0.8135702
X-RAY DIFFRACTIONf_dihedral_angle_d13.7032441
X-RAY DIFFRACTIONf_chiral_restr0.05637
X-RAY DIFFRACTIONf_plane_restr0.005736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7888-1.81240.26721300.24523188X-RAY DIFFRACTION88
1.8124-1.83720.24371410.2133223X-RAY DIFFRACTION91
1.8372-1.86350.27751340.22573376X-RAY DIFFRACTION90
1.8635-1.89130.24061330.20833313X-RAY DIFFRACTION92
1.8913-1.92080.21111340.19763278X-RAY DIFFRACTION90
1.9208-1.95230.21011370.18833316X-RAY DIFFRACTION90
1.9523-1.9860.21091350.18183346X-RAY DIFFRACTION92
1.986-2.02210.22491400.18153341X-RAY DIFFRACTION91
2.0221-2.0610.19531380.1773344X-RAY DIFFRACTION93
2.061-2.10310.20021360.17753306X-RAY DIFFRACTION89
2.1031-2.14880.17781410.16913317X-RAY DIFFRACTION92
2.1488-2.19880.20251390.16763374X-RAY DIFFRACTION92
2.1988-2.25380.16931340.17133329X-RAY DIFFRACTION91
2.2538-2.31470.15821420.16213392X-RAY DIFFRACTION92
2.3147-2.38280.22211390.1653375X-RAY DIFFRACTION93
2.3828-2.45970.19891430.15683421X-RAY DIFFRACTION93
2.4597-2.54760.15631370.16233440X-RAY DIFFRACTION94
2.5476-2.64960.17151400.16273434X-RAY DIFFRACTION94
2.6496-2.77020.20281370.15963384X-RAY DIFFRACTION93
2.7702-2.91620.18361420.16393457X-RAY DIFFRACTION93
2.9162-3.09890.17331420.16473416X-RAY DIFFRACTION94
3.0989-3.33810.18851450.16063474X-RAY DIFFRACTION95
3.3381-3.67390.15541440.15153426X-RAY DIFFRACTION94
3.6739-4.20520.1741420.14483387X-RAY DIFFRACTION93
4.2052-5.2970.13871420.13663522X-RAY DIFFRACTION96
5.297-46.67190.20211490.18133598X-RAY DIFFRACTION98

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