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- PDB-6v2l: E. coli Phosphoenolpyruvate carboxykinase S250A -

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Basic information

Entry
Database: PDB / ID: 6v2l
TitleE. coli Phosphoenolpyruvate carboxykinase S250A
ComponentsPhosphoenolpyruvate carboxykinase (ATP)
KeywordsLYASE
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / kinase activity / calcium ion binding / magnesium ion binding / ATP binding / metal ion binding / cytoplasm / 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
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / : / Phosphoenolpyruvate carboxykinase (ATP) / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSokaribo, A.S. / Goldie, H. / Sanders, D.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Kinetic and structural analysis of Escherichia coli phosphoenolpyruvate carboxykinase mutants.
Authors: Sokaribo, A. / Novakovski, B.A.A. / Cotelesage, J. / White, A.P. / Sanders, D. / Goldie, H.
History
DepositionNov 25, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionDec 11, 2019ID: 6D5I
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2Oct 11, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)60,4155
Polymers59,7391
Non-polymers6764
Water9,926551
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.910, 94.620, 46.350
Angle α, β, γ (deg.)90.000, 96.210, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-762-

HOH

21A-996-

HOH

31A-1056-

HOH

41A-1158-

HOH

51A-1165-

HOH

61A-1204-

HOH

71A-1222-

HOH

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Components

#1: Protein Phosphoenolpyruvate carboxykinase (ATP) / PEPCK


Mass: 59739.270 Da / Num. of mol.: 1 / Mutation: S250A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pckA, D9G24_04840 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A400L9R1, UniProt: P22259*PLUS, phosphoenolpyruvate carboxykinase (ATP)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: microbatch
Details: A 2ul drop with 3 mg/ml S250A PCK, 5 mM Manganese chloride, 5mM Magnesium chloride, 2 mM ATP, 2mM Pyruvate, 1 mM EDTA, 200 mM Ammonium acetate, 100 mM Sodium acetate pH 4.8, 0.01 mM DTT, 12% ...Details: A 2ul drop with 3 mg/ml S250A PCK, 5 mM Manganese chloride, 5mM Magnesium chloride, 2 mM ATP, 2mM Pyruvate, 1 mM EDTA, 200 mM Ammonium acetate, 100 mM Sodium acetate pH 4.8, 0.01 mM DTT, 12% PEG 4000 was added to 2 ul drop containing 0.01 mM Nickel chloride, 0.1 M Tris pH 8.5, 20% PEG 2000. After a week a rod like crystal was removed and soaked in a solution with 30% glycerol 1mM EDTA, 100 mM sodium acetate 200mM ammonium acetate and 12% PEG 4000 for 10 seconds and flash cooled in liquid notrogen

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.8856 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.7→40.5 Å / Num. obs: 58603 / % possible obs: 99.59 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.05 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1803 / Rpim(I) all: 0.1056 / Rrim(I) all: 0.2092 / Net I/σ(I): 9.63
Reflection shellResolution: 1.7→1.761 Å / Rmerge(I) obs: 1.237 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 5814 / CC1/2: 0.491 / Rpim(I) all: 0.7255

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AYL

1ayl


Resolution: 1.7→40.5 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 2930 5 %
Rwork0.167 55666 -
obs0.1691 58596 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.42 Å2 / Biso mean: 21.3601 Å2 / Biso min: 9.09 Å2
Refinement stepCycle: final / Resolution: 1.7→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 37 551 4710
Biso mean--17.12 29.03 -
Num. residues----532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.730.32061380.29092614275299
1.73-1.760.29511400.26822656279699
1.76-1.790.2891390.262653279299
1.79-1.820.26361370.23832608274599
1.82-1.860.27821400.23152656279699
1.86-1.90.24841380.22022608274699
1.9-1.950.26471400.206626622802100
1.95-1.990.23251380.194226282766100
1.99-2.050.25371390.17962636277599
2.05-2.110.21311410.174826702811100
2.11-2.180.23351380.158826272765100
2.18-2.250.19581390.160226512790100
2.25-2.340.2131390.16022630276999
2.34-2.450.22071410.164826892830100
2.45-2.580.20071400.161726472787100
2.58-2.740.22791390.165426492788100
2.74-2.950.1941400.15826522792100
2.95-3.250.20251400.152126752815100
3.25-3.720.15381410.139226662807100
3.72-4.690.17151410.123426812822100
4.69-40.50.17221420.15112708285099

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