7EZB

Thorarchaeota Rab bound to GDP

PDB DOI: https://doi.org/10.2210/pdb7EZB/pdb

Classification: SIGNALING PROTEIN
Organism(s): Candidatus Thorarchaeota archaeon SMTZ1-45
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-06-01 Released: 2022-06-08
Deposition Author(s): Robinson, R.C., Tran, L.T.
Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS), Moore and Simons foundations

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.174
R-Value Work: 0.154

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of Thor-Rab

Robinson, R.C., Tran, L.T.

To be published.

Macromolecule Content

Total Structure Weight: 42.71 kDa
Atom Count: 3,403
Modelled Residue Count: 345
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thorarchaeota Rab	A, B	182	Candidatus Thorarchaeota archaeon SMTZ1-45	Mutation(s): 0 Gene Names: AM325_13980
UniProt
Find proteins for A0A135VL07 (Candidatus Thorarchaeota archaeon SMTZ1-45) Explore A0A135VL07 Go to UniProtKB: A0A135VL07
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A135VL07
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.174
R-Value Work: 0.154
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.791	α = 90
b = 68.791	β = 90
c = 66.346	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-08

Deposition Author(s):

Robinson, R.C.

Tran, L.T.

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR19S5
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H00476
Moore and Simons foundations	United States	GBMF9743

Revision History (Full details and data files)

Version 1.0: 2022-06-08
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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Help and Resources

7EZB

Thorarchaeota Rab bound to GDP

Structure of Thor-Rab

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)