6V3O

Crystal structure of the T-state of maize C4-phosphoenolpyruvate carboxylase in complex with citrate

PDB DOI: https://doi.org/10.2210/pdb6V3O/pdb

Classification: LYASE
Organism(s): Zea mays
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2019-11-26 Released: 2020-12-09
Deposition Author(s): Carrizosa-Carbajal, E.I., Munoz-Clares, R.A., Gonzalez-Segura, L.
Funding Organization(s): Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.249
R-Value Work: 0.218
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structures of the T-state of maize C4-phosphoenolpyruvate carboxylase provides insight into the Structural basis of the allosteric transition of plant phosphoenolpyruvate carboxylase enzymes

Carrizosa-Carbajal, E.I., Gonzalez-Segura, L., Munoz-Clares, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 879.42 kDa
Atom Count: 59,688
Modelled Residue Count: 7,480
Deposited Residue Count: 7,760
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxylase	A, B, C, D, E A, B, C, D, E, F, G, H	970	Zea mays	Mutation(s): 0 Gene Names: ppc1 EC: 4.1.1.31
UniProt
Find proteins for P04711 (Zea mays) Explore P04711 Go to UniProtKB: P04711
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04711
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth F] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C]	AA [auth E] EA [auth F] L [auth A] O [auth B] P [auth B] AA [auth E], EA [auth F], L [auth A], O [auth B], P [auth B], S [auth C]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C]
PG0 Query on PG0 Download Ideal Coordinates CCD File SDF format, chain T [auth D] MOL2 format, chain T [auth D]	T [auth D]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain T [auth D] Interactions & Density Focus chain T [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain I [auth A] SDF format, chain IA [auth G] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth H] SDF format, chain LA [auth H] SDF format, chain M [auth B] SDF format, chain MA [auth H] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E]	BA [auth F] CA [auth F] DA [auth F] GA [auth G] HA [auth G] BA [auth F], CA [auth F], DA [auth F], GA [auth G], HA [auth G], I [auth A], IA [auth G], J [auth A], K [auth A], KA [auth H], LA [auth H], M [auth B], MA [auth H], N [auth B], Q [auth C], R [auth C], U [auth D], V [auth D], W [auth D], X [auth E], Y [auth E], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain M [auth B] Focus chain MA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain M [auth B] Focus chain MA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain JA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain JA [auth H]	FA [auth G], JA [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth G] Focus chain JA [auth H] Interactions & Density Focus chain FA [auth G] Focus chain JA [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.249
R-Value Work: 0.218
R-Value Observed: 0.220
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.692	α = 90
b = 217.976	β = 91.05
c = 173.569	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Carrizosa-Carbajal, E.I.

Munoz-Clares, R.A.

Gonzalez-Segura, L.

Funding Organization	Location	Grant Number
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)	Mexico	IN227920

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2023-03-29
Changes: Author supporting evidence, Database references
Version 1.2: 2023-05-17
Changes: Author supporting evidence
Version 1.3: 2023-10-25
Changes: Data collection, Refinement description