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- PDB-6crt: Arg65Gln Mutagenic E.coli PCK -

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Basic information

Entry
Database: PDB / ID: 6crt
TitleArg65Gln Mutagenic E.coli PCK
ComponentsPhosphoenolpyruvate carboxykinase (ATP)Phosphoenolpyruvate carboxykinase (ATP)
KeywordsLYASE / enzyme / Pepcarboxykinase
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / 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: 1.995 Å
AuthorsSokaribo, A.S. / Cotelesage, J.H. / Novakovski, B. / Goldie, H. / Sanders, D.
CitationJournal: To Be Published
Title: Arg65Gln Mutagenic E.coli PCK
Authors: Sokaribo, A.S. / Cotelesage, J.H. / Novakovski, B. / Goldie, H. / Sanders, D.
History
DepositionMar 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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)60,2974
Polymers59,6801
Non-polymers6173
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.993, 95.301, 46.340
Angle α, β, γ (deg.)90.00, 96.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-893-

HOH

21A-947-

HOH

31A-962-

HOH

41A-1028-

HOH

51A-1058-

HOH

61A-1060-

HOH

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Components

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


Mass: 59680.113 Da / Num. of mol.: 1 / Mutation: R65Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pckA, EC55989_3809 / Production host: Escherichia coli (E. coli)
References: UniProt: B7L4T1, 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-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 2 ul drop containing 8 mg/ml Arg65Gln E.coli PCK, 5 mM MnCl2, 5 mM MgCl2, 2mM ATP, 2mM pyruvate, 1mM EDTA, 200 mM ammonium acetate, 100 mM sodium acetate pH 4.4 and 12% PEG 4000, was added ...Details: 2 ul drop containing 8 mg/ml Arg65Gln E.coli PCK, 5 mM MnCl2, 5 mM MgCl2, 2mM ATP, 2mM pyruvate, 1mM EDTA, 200 mM ammonium acetate, 100 mM sodium acetate pH 4.4 and 12% PEG 4000, was added to 2 ul drop containing 0.2 M magnesium acetate and 20% PEG 3350. Rod like crystals formed after 7 days, and where soaked in cryoprotectant solution containing 30% glycerol, 1mM EDTA, 100 mM sodium acetae, 200 mM ammonium acetate and 12% PEG 4000 for 10 seconds and flashed cooled in liquid nitrogen

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.99→46.646 Å / Num. obs: 39657 / % possible obs: 91.5 % / Redundancy: 2.1 % / Biso Wilson estimate: 18.69 Å2 / Rmerge(I) obs: 0.35 / Net I/σ(I): 3.07
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.81

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Processing

Software
NameVersionClassification
PHENIX(dev_2398: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AYL

1ayl


Resolution: 1.995→46.051 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 2000 6.48 %
Rwork0.1565 --
obs0.16 30873 84.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.995→46.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 33 382 4550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074265
X-RAY DIFFRACTIONf_angle_d0.9335797
X-RAY DIFFRACTIONf_dihedral_angle_d11.2852518
X-RAY DIFFRACTIONf_chiral_restr0.055636
X-RAY DIFFRACTIONf_plane_restr0.006750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9951-2.0450.21631300.15891874X-RAY DIFFRACTION76
2.045-2.10030.25051480.16712134X-RAY DIFFRACTION88
2.1003-2.16210.21361460.16292117X-RAY DIFFRACTION87
2.1621-2.23190.22271480.15572132X-RAY DIFFRACTION87
2.2319-2.31170.21881480.16342141X-RAY DIFFRACTION87
2.3117-2.40420.22621430.16512071X-RAY DIFFRACTION86
2.4042-2.51360.22621460.16792094X-RAY DIFFRACTION85
2.5136-2.64620.23021440.16942081X-RAY DIFFRACTION85
2.6462-2.81190.21561430.17722068X-RAY DIFFRACTION85
2.8119-3.0290.23531450.17932084X-RAY DIFFRACTION84
3.029-3.33370.24761420.16942058X-RAY DIFFRACTION84
3.3337-3.81590.20061400.15312031X-RAY DIFFRACTION82
3.8159-4.80690.17811400.12252022X-RAY DIFFRACTION82
4.8069-46.06330.16081370.14031966X-RAY DIFFRACTION78

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