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- PDB-6v2m: Structure of Escherichia coli Asp269Asn mutant phosphoenolpyruvat... -

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Basic information

Entry
Database: PDB / ID: 6v2m
TitleStructure of Escherichia coli Asp269Asn mutant phosphoenolpyruvate carboxykinase
ComponentsPhosphoenolpyruvate carboxykinase (ATP)Phosphoenolpyruvate carboxykinase (ATP)
KeywordsLYASE / enzyme / phosphoenolpyruvate carboxykinase
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 / cytosol / cytoplasm
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
ADENOSINE-5'-TRIPHOSPHATE / Phosphoenolpyruvate carboxykinase (ATP) / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsSokaribo, A.S. / Cotelesage, J.H.
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
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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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)60,3574
Polymers59,7851
Non-polymers5723
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.780, 94.220, 46.540
Angle α, β, γ (deg.)90.000, 94.790, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-820-

HOH

21A-941-

HOH

31A-993-

HOH

41A-1010-

HOH

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Components

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


Mass: 59785.324 Da / Num. of mol.: 1 / Mutation: D269N
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 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 47 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 2ul drop with 2 mg/ml protein, 5 mM Calcium chloride, 5mM Magnesium chloride, 2 mM ATP, 2mM Pyruvate, 1 mM EDTA, 200 mM Ammonium acetate, 100 mM Sodium acetate, 0.01 mM DTT, 30% PEG 4000 was ...Details: 2ul drop with 2 mg/ml protein, 5 mM Calcium chloride, 5mM Magnesium chloride, 2 mM ATP, 2mM Pyruvate, 1 mM EDTA, 200 mM Ammonium acetate, 100 mM Sodium acetate, 0.01 mM DTT, 30% PEG 4000 was added to 2 ul drop containing 2 M sodium aceate, 0.1 M Tris pH 8.2 30% PEG 4000. 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. The crystal was put into a loop 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: 0.98 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.66→47.11 Å / Num. obs: 63107 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 26.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1151 / Rpim(I) all: 0.06368 / Rrim(I) all: 0.1318 / Net I/σ(I): 7.96
Reflection shellResolution: 1.66→1.719 Å / Redundancy: 4.2 % / Rmerge(I) obs: 2.915 / Mean I/σ(I) obs: 0.65 / Num. unique obs: 6242 / CC1/2: 0.175 / Rpim(I) all: 1.613 / Rrim(I) all: 3.34 / % possible all: 98.71

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Coot1.17.1_3660model building
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AYL

1ayl


Resolution: 1.66→46.38 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.78
RfactorNum. reflection% reflection
Rwork0.1848 --
Rfree-3152 5 %
obs-63107 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.53 Å2 / Biso mean: 30.3933 Å2 / Biso min: 15.03 Å2
Refinement stepCycle: final / Resolution: 1.66→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 33 327 4459
Biso mean--25.86 36.81 -
Num. residues----531
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.66-1.680.41691320.41112506263898
1.68-1.710.40131360.39142582271899
1.71-1.740.35821370.38326132750100
1.74-1.770.41391350.343125702705100
1.77-1.80.32211380.328726052743100
1.8-1.840.3381370.28626032740100
1.84-1.870.33371370.269726192756100
1.87-1.910.26471360.262725762712100
1.91-1.960.28141370.235926092746100
1.96-2.010.28231380.22826142752100
2.01-2.060.26581350.224525712706100
2.06-2.120.26691380.215126132751100
2.12-2.190.2371370.196226062743100
2.19-2.270.23861360.183825792715100
2.27-2.360.20681380.17626242762100
2.36-2.470.2121380.178326132751100
2.47-2.60.23571380.175926322770100
2.6-2.760.21291370.179126022739100
2.76-2.970.22631360.187125812717100
2.97-3.270.21721390.169726372776100
3.27-3.750.18721370.155826172754100
3.75-4.720.15791390.133326312770100
4.72-47.110.18581410.148626722813100

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