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- PDB-1fiy: THREE-DIMENSIONAL STRUCTURE OF PHOSPHOENOLPYRUVATE CARBOXYLASE FR... -

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Basic information

Entry
Database: PDB / ID: 1fiy
TitleTHREE-DIMENSIONAL STRUCTURE OF PHOSPHOENOLPYRUVATE CARBOXYLASE FROM ESCHERICHIA COLI AT 2.8 A RESOLUTION
ComponentsPHOSPHOENOLPYRUVATE CARBOXYLASE
KeywordsCOMPLEX (LYASE/INHIBITOR) / PHOSPHOENOLPYRUVATE / CARBOXYLASE / COMPLEX (LYASE-INHIBITOR) / COMPLEX (LYASE-INHIBITOR) complex
Function / homology
Function and homology information


phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / carbon fixation / oxaloacetate metabolic process / 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 / Phosphoenolpyruvate carboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsKai, Y. / Matsumura, H. / Inoue, T. / Terada, K. / Nagara, Y. / Yoshinaga, T. / Kihara, A. / Izui, K.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: First Crystallization of a Phosphoenolpyruvate Carboxylase from Escherichia Coli
Authors: Inoue, M. / Hayashi, M. / Sugimoto, M. / Harada, S. / Kai, Y. / Kasai, N. / Terada, K. / Izui, K.
History
DepositionMay 2, 1998Processing site: BNL
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4Feb 7, 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)99,3092
Polymers99,1751
Non-polymers1331
Water70339
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)397,2348
Polymers396,7024
Non-polymers5324
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)117.600, 248.400, 82.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PHOSPHOENOLPYRUVATE CARBOXYLASE / / PEPC


Mass: 99175.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12
References: UniProt: P00864, phosphoenolpyruvate carboxylase
#2: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRESIDUE ASP 884 IS AN ALLOSTERIC INHIBITOR. THIS GROUP IS ASSIGNED AS A SEPARATE STANDARD-ALONE ...RESIDUE ASP 884 IS AN ALLOSTERIC INHIBITOR. THIS GROUP IS ASSIGNED AS A SEPARATE STANDARD-ALONE RESIDUE WITH THE CHAIN ID "L".

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMTris-HCl1drop
36 mMsodium-L-aspartate1drop
445 mM1dropCaCl2
50.6 mMdithiothreitol1drop
610 %(w/v)PEG3001drop
72.5 mML-aspartate1reservoir
890 mM1reservoirCaCl2
90.25 mMdithiothreitol1reservoir
1015 %(w/v)PEG3001reservoir
1150 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 15, 1996 / Details: SYNCHROTRON RADIATION
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 28509 / % possible obs: 93.3 % / Observed criterion σ(I): 0.5 / Redundancy: 3.6 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.251 / % possible all: 87.5
Reflection shell
*PLUS
% possible obs: 87.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
MLPHAREphasing
REFMACrefinement
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→10 Å
RfactorNum. reflection% reflection
Rfree0.259 1409 5 %
obs0.219 26242 -
Displacement parametersBiso mean: 41.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6888 0 9 39 6936
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0260.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3032
X-RAY DIFFRACTIONp_mcangle_it2.293
X-RAY DIFFRACTIONp_scbond_it1.4732
X-RAY DIFFRACTIONp_scangle_it2.4993
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1440.14
X-RAY DIFFRACTIONp_singtor_nbd0.1940.3
X-RAY DIFFRACTIONp_multtor_nbd0.2730.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1770.3
X-RAY DIFFRACTIONp_planar_tor6.22
X-RAY DIFFRACTIONp_staggered_tor2615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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