2QJL | pdb_00002qjl

Crystal structure of Urm1

• PDB DOI: https://doi.org/10.2210/pdb2QJL/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-07-07 Released: 2007-07-17 
• Deposition Author(s): Yu, J., Zhou, C.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.198 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the dimeric Urm1 from the yeast Saccharomyces cerevisiae.

Yu, J., Zhou, C.Z.

(2008) Proteins 71: 1050-1055

• PubMed: 18260097 
• DOI: https://doi.org/10.1002/prot.21975
• Primary Citation Related Structures: 
  2QJL

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Organizational Affiliation: 
• Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.15 kDa 
• Atom Count: 1,070 
• Modeled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-related modifier 1	A	99	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: Urm1
UniProt
Find proteins for P40554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40554  Go to UniProtKB:  P40554

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.198 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.384	α = 90
b = 63.009	β = 90
c = 28.893	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
AUTOMAR	data reduction
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-17 
Deposition Author(s): Yu, J., Zhou, C.Z.

Revision History  

• Version 1.0: 2007-07-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description