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- PDB-2zci: Structure of a GTP-dependent bacterial PEP-carboxykinase from Cor... -

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Basic information

Entry
Database: PDB / ID: 2zci
TitleStructure of a GTP-dependent bacterial PEP-carboxykinase from Corynebacterium glutamicum
ComponentsPhosphoenolpyruvate carboxykinase [GTP]
KeywordsSIGNALING PROTEIN / LYASE / GTP-dependent / carboxykinase
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / gluconeogenesis / manganese ion binding / GTP binding / cytoplasm
Similarity search - Function
Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 ...Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) 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
Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAich, S. / Prasad, L. / Delbaere, L.T.J.
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2008
Title: Structure of a GTP-dependent bacterial PEP-carboxykinase from Corynebacterium glutamicum.
Authors: Aich, S. / Prasad, L. / Delbaere, L.T.
History
DepositionNov 9, 2007Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 [GTP]
B: Phosphoenolpyruvate carboxykinase [GTP]
C: Phosphoenolpyruvate carboxykinase [GTP]
D: Phosphoenolpyruvate carboxykinase [GTP]


Theoretical massNumber of molelcules
Total (without water)267,7484
Polymers267,7484
Non-polymers00
Water5,873326
1
A: Phosphoenolpyruvate carboxykinase [GTP]
C: Phosphoenolpyruvate carboxykinase [GTP]


Theoretical massNumber of molelcules
Total (without water)133,8742
Polymers133,8742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-4.9 kcal/mol
Surface area41390 Å2
MethodPISA
2
B: Phosphoenolpyruvate carboxykinase [GTP]
D: Phosphoenolpyruvate carboxykinase [GTP]


Theoretical massNumber of molelcules
Total (without water)133,8742
Polymers133,8742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-6.5 kcal/mol
Surface area41000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.336, 118.055, 152.931
Angle α, β, γ (deg.)90.00, 96.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphoenolpyruvate carboxykinase [GTP] / E.C.4.1.1.32 / PEP carboxykinase / Phosphoenolpyruvate carboxylase / PEPCK


Mass: 66937.117 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: gene pckG, pck / Source: (natural) Corynebacterium glutamicum (bacteria)
References: UniProt: Q9AEM1, phosphoenolpyruvate carboxykinase (GTP)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG 4000, 0.1M sodium acetate, 0.2M ammonium acetate, 10mM MgCl2, 1mM MnCl2, 2mM EDTA, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9984 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 18, 2003
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9984 Å / Relative weight: 1
ReflectionResolution: 2.1→28 Å / Num. all: 144542 / Num. obs: 144542 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.1 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 3.1 / Num. unique all: 6867 / Rsym value: 0.75 / % possible all: 78

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1KHF

1khf


Resolution: 2.3→24.83 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.882 / SU B: 8.68 / SU ML: 0.211 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.783 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27884 4256 5 %RANDOM
Rwork0.18769 ---
all0.19226 80542 --
obs0.19226 80542 77.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.03 Å2
2--0 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18081 0 0 326 18407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.02218558
X-RAY DIFFRACTIONr_angle_refined_deg2.4931.94625266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.14352325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59524.861864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.134152925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6161592
X-RAY DIFFRACTIONr_chiral_restr0.1750.22680
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214476
X-RAY DIFFRACTIONr_nbd_refined0.260.29287
X-RAY DIFFRACTIONr_nbtor_refined0.320.212112
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2833
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3610.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.26
X-RAY DIFFRACTIONr_mcbond_it1.2921.512048
X-RAY DIFFRACTIONr_mcangle_it2.074218623
X-RAY DIFFRACTIONr_scbond_it3.2337842
X-RAY DIFFRACTIONr_scangle_it4.584.56643
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 285 -
Rwork0.226 5591 -
obs--72.83 %

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