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- PDB-1jqo: Crystal structure of C4-form phosphoenolpyruvate carboxylase from... -

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Basic information

Entry
Database: PDB / ID: 1jqo
TitleCrystal structure of C4-form phosphoenolpyruvate carboxylase from maize
Componentsphosphoenolpyruvate carboxylase
KeywordsLYASE / BETA BARREL / Carbon dioxide fixation
Function / homology
Function and homology information


response to cytokinin / phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / response to nitrate / leaf development / response to ammonium ion / carbon fixation / photosynthesis / tricarboxylic acid cycle / cytosol
Similarity search - Function
Phosphoenolpyruvate/pyruvate domain / 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. / de novo design (two linked rop proteins) / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily ...Phosphoenolpyruvate/pyruvate domain / 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. / de novo design (two linked rop proteins) / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphoenolpyruvate carboxylase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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: Derived calculations / Version format compliance
Revision 1.3Mar 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
B: phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,0644
Polymers218,8722
Non-polymers1922
Water00
1
A: phosphoenolpyruvate carboxylase
B: phosphoenolpyruvate carboxylase
hetero molecules

A: phosphoenolpyruvate carboxylase
B: phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)438,1288
Polymers437,7444
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-31 kcal/mol
Surface area68130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)158.440, 174.610, 254.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer generated from dimer in the assymmetric unit by two fole axis.

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Components

#1: Protein phosphoenolpyruvate carboxylase / PHOSPHOENOLPYRUVATE CARBOXYLASE 1 / PEPCASE


Mass: 109436.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / Strain: B37 / Tissue: leaves
References: UniProt: P04711, phosphoenolpyruvate carboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, Tris-HCl, LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
31 mMdithiothreitol1drop
420 %ethylene glycol1drop
55 mMmalate1drop
612 %PEG80001reservoir
7400 mM1reservoirLi2SO4
820 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Mar 25, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 3→86.2 Å / Num. all: 266008 / Num. obs: 58078 / % possible obs: 80.4 % / Observed criterion σ(I): 7.4 / Rmerge(I) obs: 0.091
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.309 / % possible all: 57.7
Reflection
*PLUS
Num. measured all: 266008

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→86.2 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2893 5 %RANDOM
Rwork0.236 ---
all-57271 --
obs-57271 --
Refine analyzeLuzzati coordinate error obs: 0.43 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 1.06 Å
Refinement stepCycle: LAST / Resolution: 3→86.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14424 0 10 0 14434
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 3→3.14 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.415 -3 %
Rwork0.413 --
obs-6900 60.5 %
Refinement
*PLUS
Highest resolution: 3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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