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- PDB-6v2n: Crystal structure of E. coli phosphoenolpyruvate carboxykinase mu... -

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Basic information

Entry
Database: PDB / ID: 6v2n
TitleCrystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys254Ser
ComponentsPhosphoenolpyruvate carboxykinase (ATP)Phosphoenolpyruvate carboxykinase (ATP)
KeywordsLYASE / enzyme / Pepcarboxykinase
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
ACETATE ION / Phosphoenolpyruvate carboxykinase (ATP) / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSokaribo, A.S. / Cotelesage, J.H. / Novakovski, B. / 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 25, 2019ID: 6CU4
Revision 1.0Dec 25, 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.ptnr2_auth_seq_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)59,5323
Polymers59,4331
Non-polymers992
Water9,422523
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)54.906, 76.647, 65.421
Angle α, β, γ (deg.)90.000, 96.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 59432.723 Da / Num. of mol.: 1
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 2 ul drop containing 2 mg/ml Lys254Ser E. coli PCK, 5 mM MnCl2, 5mM MgCl2, 2mM ATP, 2mM pyruvate, 1 mM EDTA, 200 mM ammonium acetate, 100 mM sodium acetate pH 4.8, 0.01 mM DTT and 10% PEG ...Details: 2 ul drop containing 2 mg/ml Lys254Ser E. coli PCK, 5 mM MnCl2, 5mM MgCl2, 2mM ATP, 2mM pyruvate, 1 mM EDTA, 200 mM ammonium acetate, 100 mM sodium acetate pH 4.8, 0.01 mM DTT and 10% PEG 4000, was added to 2 ul drop containing 0.2 M calcium chloride and 20% PEG. Rod like crystals formed after 7 days, were harvested, and soaked in cryoprotectant solution (30% glycerol, 1mM EDTA, 100 mM sodium acetate, 200 mM ammonium acetate and 12% PEG 4000) for 10 seconds and flash cooled in liquid nitrogen

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→44.45 Å / Num. obs: 64733 / % possible obs: 99.83 % / Redundancy: 5.1 % / Biso Wilson estimate: 13.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07574 / Rpim(I) all: 0.03608 / Rrim(I) all: 0.08409 / Net I/σ(I): 14.67
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.3185 / Mean I/σ(I) obs: 4.56 / Num. unique obs: 6479 / CC1/2: 0.953 / Rpim(I) all: 0.1576 / Rrim(I) all: 0.3562 / % possible all: 99.92

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Processing

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

1oen


Resolution: 1.65→44.29 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.52
RfactorNum. reflection% reflection
Rfree0.1743 1353 2.09 %
Rwork0.1459 --
obs0.1465 64727 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.74 Å2 / Biso mean: 19.5675 Å2 / Biso min: 5.01 Å2
Refinement stepCycle: final / Resolution: 1.65→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 5 523 4553
Biso mean--19.71 31.03 -
Num. residues----518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.65-1.710.21011360.16526343
1.71-1.780.19591340.15426290
1.78-1.860.18571350.14536316
1.86-1.960.19961350.14186319
1.96-2.080.16321340.14116291
2.08-2.240.19481350.14126350
2.24-2.460.15741360.14596323
2.46-2.820.21531340.15246322
2.82-3.550.17481360.14646365
3.55-44.290.141380.14246455
Refinement TLS params.Method: refined / Origin x: 12.5846 Å / Origin y: -0.3319 Å / Origin z: 11.8894 Å
111213212223313233
T0.0467 Å20.0077 Å2-0.0061 Å2-0.0558 Å2-0.0111 Å2--0.0635 Å2
L0.2069 °2-0.0137 °2-0.0017 °2-0.2607 °2-0.0197 °2--0.4968 °2
S0.0001 Å °-0.0261 Å °0.0273 Å °0.0425 Å °0.0104 Å °-0.0391 Å °0.0191 Å °0.0152 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 540
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allS1 - 649

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