4BXH | pdb_00004bxh

Resolving the activation site of positive regulators in plant phosphoenolpyruvate carboxylase

• PDB DOI: https://doi.org/10.2210/pdb4BXH/pdb

• Classification: LYASE
• Organism(s): Flaveria trinervia
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-11 Released: 2013-10-02 
• Deposition Author(s): Schlieper, D., Foerster, K., Paulus, J.K., Groth, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.210 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Resolving the Activation Site of Positive Regulators in Plant Phosphoenolpyruvate Carboxylase.

Schlieper, D., Foerster, K., Paulus, J.K., Groth, G.

(2014) Mol Plant 7: 437

• PubMed: 24043710 
• DOI: https://doi.org/10.1093/mp/sst130
• Primary Citation Related Structures: 
  4BXC, 4BXH

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Organizational Affiliation: 
• Institute of Biochemical Plant Physiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 227.41 kDa 
• Atom Count: 15,803 
• Modeled Residue Count: 1,856 
• Deposited Residue Count: 1,980 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C4 PHOSPHOENOLPYRUVATE CARBOXYLASE	A	990	Flaveria trinervia	Mutation(s): 0  EC: 4.1.1.31
UniProt
Find proteins for P30694 (Flaveria trinervia) Explore P30694  Go to UniProtKB:  P30694

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C4 PHOSPHOENOLPYRUVATE CARBOXYLASE	B	990	Flaveria trinervia	Mutation(s): 0  EC: 4.1.1.31
UniProt
Find proteins for P30694 (Flaveria trinervia) Explore P30694  Go to UniProtKB:  P30694

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.210 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.918	α = 90
b = 122.857	β = 90
c = 131.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Schlieper, D., Foerster, K., Paulus, J.K., Groth, G.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2013-12-04
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2014-02-05
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description