5U9L | pdb_00005u9l

Crystal structure of the intermembrane space region of the plastid division protein PARC6

PDB DOI: https://doi.org/10.2210/pdb5U9L/pdb

Classification: CELL CYCLE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-16 Released: 2017-12-20
Deposition Author(s): Delmar, J.D., Chou, T.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.259 (Depositor), 0.263 (DCC)
R-Value Work:
0.181 (Depositor), 0.185 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5U9L

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

Literature

Cocrystal structure of the intermembrane space region of the plastid division proteins PARC6 and PDV1

Delmar, J.A., Yu, E.W., Osteryoung, K.W.

To be published.

Macromolecule Content

Total Structure Weight: 53.12 kDa
Atom Count: 2,514
Modeled Residue Count: 303
Deposited Residue Count: 466
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PARALOG OF ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6 (PARC6)	A, B	233	Arabidopsis thaliana	Mutation(s): 0 Gene Names: CDP1, ARC6H, PARC6, At3g19180, MVI11.9
UniProt
Find proteins for Q8VY16 (Arabidopsis thaliana) Explore Q8VY16 Go to UniProtKB: Q8VY16
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8VY16
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.259 (Depositor), 0.263 (DCC)
R-Value Work: 0.181 (Depositor), 0.185 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.533	α = 90
b = 124.546	β = 90
c = 130.046	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.