7ZY7 | pdb_00007zy7

Crystal structure of Chlamydomonas reinhardtii chloroplastic phosphoglycerate kinase

PDB DOI: https://doi.org/10.2210/pdb7ZY7/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Chlamydomonas reinhardtii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-24 Released: 2023-06-14
Deposition Author(s): Le Moigne, T., Lemaire, S.D., Henri, J.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Chlamydomonas reinhardtii chloroplastic phosphoglycerate kinase

Le Moigne, T., Lemaire, S.D., Henri, J.

To be published.

Macromolecule Content

Total Structure Weight: 88.15 kDa
Atom Count: 6,419
Modeled Residue Count: 788
Deposited Residue Count: 822
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate kinase	A, B	411	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: PGK1, CHLRE_11g467770v5, CHLREDRAFT_132210 EC: 2.7.2.3
UniProt
Find proteins for A8JC04 (Chlamydomonas reinhardtii) Explore A8JC04 Go to UniProtKB: A8JC04
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8JC04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B]	C [auth A], D [auth B], E [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.226 (Depositor), 0.230 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.851	α = 90
b = 53.138	β = 90.7
c = 66.406	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	--

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.