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- PDB-1jqn: Crystal structure of E.coli phosphoenolpyruvate carboxylase in co... -

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Basic information

Entry
Database: PDB / ID: 1jqn
TitleCrystal structure of E.coli phosphoenolpyruvate carboxylase in complex with Mn2+ and DCDP
Componentsphosphoenolpyruvate carboxylase
KeywordsLYASE / BETA BARREL / Mn2+ and DCDP COMPLEX
Function / homology
Function and homology information


phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / oxaloacetate metabolic process / carbon fixation / tricarboxylic acid cycle / gluconeogenesis / protein homotetramerization / magnesium ion binding / identical protein binding / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxylase, Lys active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase, bacterial/plant-type / Phosphoenolpyruvate carboxylase, His active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase active site 2. / Phosphoenolpyruvate carboxylase active site 1. / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
ASPARTIC ACID / 3,3-DICHLORO-2-PHOSPHONOMETHYL-ACRYLIC ACID / : / Phosphoenolpyruvate carboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMatsumura, H. / Kai, Y.
Citation
Journal: Structure / Year: 2002
Title: Crystal structures of C4 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases.
Authors: Matsumura, H. / Xie, Y. / Shirakata, S. / Inoue, T. / Yoshinaga, T. / Ueno, Y. / Izui, K. / Kai, Y.
#1: Journal: FEBS Lett. / Year: 1999
Title: Plausible phosphoenolpyruvate binding site revealed by 2.6 A structure of Mn2+-bound phosphoenolpyruvate carboxylase from Escherichia coli.
Authors: Matsumura, H. / Terada, M. / Shirakata, S. / Inoue, T. / Yoshinaga, T. / Izui, K. / Kai, Y.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Three-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition
Authors: Kai, Y. / Matsumura, H. / Inoue, T. / Terada, K. / Nagara, Y. / Yoshinaga, T. / Kihara, A. / Tsumura, K. / Izui, K.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary x-ray diffraction studies of C4-form phosphoenolpyruvate carboxylase from maize diffraction studies of C4-form phosphoenolpyruvate carboxylase from maize.
Authors: Matsumura, H. / Nagata, T. / Terada, M. / Shirakata, S. / Inoue, T. / Yoshinaga, T. / Ueno, Y. / Saze, H. / Izui, K. / Kai, Y.
History
DepositionAug 7, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] ..._pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5984
Polymers99,1751
Non-polymers4233
Water3,495194
1
A: phosphoenolpyruvate carboxylase
hetero molecules

A: phosphoenolpyruvate carboxylase
hetero molecules

A: phosphoenolpyruvate carboxylase
hetero molecules

A: phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,39416
Polymers396,7024
Non-polymers1,69212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)117.950, 249.060, 83.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a tetramer generated from monomer in the assymmetric unit by D2 symmetry.

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Components

#1: Protein phosphoenolpyruvate carboxylase / PEPCASE / PEPC


Mass: 99175.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Escherichia coli / Production host: Escherichia coli (E. coli) / Strain (production host): F15
References: UniProt: P00864, phosphoenolpyruvate carboxylase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical ChemComp-DCO / 3,3-DICHLORO-2-PHOSPHONOMETHYL-ACRYLIC ACID


Mass: 234.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5Cl2O5P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG300, Tris-HCl, MnCl2, DCDP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19 mg/mlprotein1drop
250 mMTris-HCl1droppH7.4
31 mMdithiothreitol1drop
410 mMaspartate1drop
550 mMTris-HCl1reservoirpH7.4
60.6 mMdithiothreitol1reservoir
710 mMaspartate1reservoir
80.6 Msucrose1reservoir
945 mM1reservoirMnSO4
1010 mMDCDP1reservoir
1115 %(w/v)PEG3001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 24, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→39.5 Å / Num. all: 233027 / Num. obs: 45789 / % possible obs: 89.2 % / Observed criterion σ(I): 11.3 / Rmerge(I) obs: 0.058
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.302 / % possible all: 61.9
Reflection
*PLUS
Num. measured all: 233027

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39.5 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2292 5 %RANDOM
Rwork0.195 ---
all-45753 --
obs-45753 --
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.56 Å
Refinement stepCycle: LAST / Resolution: 2.35→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6881 0 22 194 7097
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.37 300 -
Rwork0.357 --
obs-5343 66.8 %
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Lowest resolution: 2.5 Å

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