5DE3 | pdb_00005de3

The Crystal structure of Chlamydomonas reinhardtii Arl3 bound to GppNHp

PDB DOI: https://doi.org/10.2210/pdb5DE3/pdb

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

Deposited: 2015-08-25 Released: 2016-09-14
Deposition Author(s): Gotthardt, K., Lokaj, M., Wittinghofer, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.228 (Depositor), 0.227 (DCC)
R-Value Work:
0.207 (Depositor), 0.208 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

The Crystal structure of Chlamydomonas reinhardtii Arl3 bound to GppNHp

Gotthardt, K., Lokaj, M., Wittinghofer, A.

To be published.

Macromolecule Content

Total Structure Weight: 19.67 kDa
Atom Count: 1,402
Modeled Residue Count: 166
Deposited Residue Count: 169
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor-like protein 3	A	169	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: ARL3, CHLREDRAFT_128761
UniProt
Find proteins for A8ISN6 (Chlamydomonas reinhardtii) Explore A8ISN6 Go to UniProtKB: A8ISN6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8ISN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.228 (Depositor), 0.227 (DCC)
R-Value Work: 0.207 (Depositor), 0.208 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.84	α = 90
b = 43.33	β = 90
c = 80.85	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Wittinghofer, A.

Revision History (Full details and data files)

Version 1.0: 2016-09-14
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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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.