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- PDB-6asn: E. coli phosphoenolpyruvate carboxykinase K212I F216V mutant boun... -

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Basic information

Entry
Database: PDB / ID: 6asn
TitleE. coli phosphoenolpyruvate carboxykinase K212I F216V 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-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal ...Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / 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 / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.549 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 25, 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
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase (ATP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8585
Polymers60,4741
Non-polymers3844
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.843, 75.605, 71.530
Angle α, β, γ (deg.)90.00, 94.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 60474.004 Da / Num. of mol.: 1 / Mutation: K212I, F216V
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)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.16 M ammonium sulfate, 0.08 M sodium acetate pH 4.8, 20% PEG 4000, 15% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.549→47.304 Å / Num. obs: 168368 / % possible obs: 91.1 % / Redundancy: 3.76 % / Net I/σ(I): 9.08

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.549→47.304 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.26
RfactorNum. reflection% reflection
Rfree0.1931 3945 2.35 %
Rwork0.1743 --
obs0.1748 168225 91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.549→47.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 0 20 264 4346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094207
X-RAY DIFFRACTIONf_angle_d0.9735729
X-RAY DIFFRACTIONf_dihedral_angle_d10.542474
X-RAY DIFFRACTIONf_chiral_restr0.058633
X-RAY DIFFRACTIONf_plane_restr0.007744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5494-1.56830.3357690.36213053X-RAY DIFFRACTION47
1.5683-1.58810.3178910.34693602X-RAY DIFFRACTION55
1.5881-1.6090.3535940.33663942X-RAY DIFFRACTION62
1.609-1.63110.33571030.32164430X-RAY DIFFRACTION69
1.6311-1.65440.38421240.3055083X-RAY DIFFRACTION78
1.6544-1.67910.30161480.28945957X-RAY DIFFRACTION93
1.6791-1.70530.30011360.2786157X-RAY DIFFRACTION96
1.7053-1.73330.26891410.26266174X-RAY DIFFRACTION96
1.7333-1.76320.27071490.25896264X-RAY DIFFRACTION97
1.7632-1.79520.24711600.24576168X-RAY DIFFRACTION96
1.7952-1.82980.29381360.22486195X-RAY DIFFRACTION97
1.8298-1.86710.30561570.21076202X-RAY DIFFRACTION97
1.8671-1.90770.25381260.19346214X-RAY DIFFRACTION96
1.9077-1.95210.17261520.18226281X-RAY DIFFRACTION97
1.9521-2.00090.21551610.17446269X-RAY DIFFRACTION97
2.0009-2.0550.17831570.16686247X-RAY DIFFRACTION97
2.055-2.11550.18751430.15996255X-RAY DIFFRACTION97
2.1155-2.18380.14651490.15146254X-RAY DIFFRACTION97
2.1838-2.26180.17731560.1566332X-RAY DIFFRACTION98
2.2618-2.35240.18971480.15456350X-RAY DIFFRACTION98
2.3524-2.45940.18481570.15576242X-RAY DIFFRACTION98
2.4594-2.58910.19121630.15786339X-RAY DIFFRACTION98
2.5891-2.75130.21491510.16316370X-RAY DIFFRACTION98
2.7513-2.96370.16841490.16776365X-RAY DIFFRACTION99
2.9637-3.26190.17311610.15956377X-RAY DIFFRACTION99
3.2619-3.73370.19561660.15726361X-RAY DIFFRACTION99
3.7337-4.70340.12541480.13496391X-RAY DIFFRACTION99
4.7034-47.32570.16011500.15656406X-RAY DIFFRACTION100

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