5GOD | pdb_00005god

Lys27-linked di-ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb5GOD/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2016-07-26 Released: 2016-11-02 
• Deposition Author(s): Gao, S., Pan, M., Zheng, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Monomer/Oligomer Quasi-Racemic Protein Crystallography

Gao, S., Pan, M., Zheng, Y., Huang, Y., Zheng, Q., Sun, D., Lu, L., Tan, X., Tan, X., Lan, H., Wang, J., Wang, T., Wang, J., Liu, L.

(2016) J Am Chem Soc 138: 14497-14502

• PubMed: 27768314 
• DOI: https://doi.org/10.1021/jacs.6b09545
• Primary Citation Related Structures: 
  5GO7, 5GO8, 5GOB, 5GOC, 5GOD, 5GOG, 5GOH, 5GOI, 5GOJ, 5GOK


• PubMed Abstract: 
  

  Racemic or quasi-racemic crystallography recently emerges as a useful technology for solution of the crystal structures of biomacromolecules. It remains unclear to what extent the biomacromolecules of opposite handedness can differ from each other in racemic or quasi-racemic crystallography. Here we report a finding that monomeric d-ubiquitin (Ub) has propensity to cocrystallize with different dimers, trimers, and even a tetramer of l-Ub. In these cocrystals the unconnected monomeric d-Ubs can self-assemble to form pseudomirror images of different oligomers of l-Ub. This monomer/oligomer cocrystallization phenomenon expands the concept of racemic crystallography. Using the monomer/oligomer cocrystallization technology we obtained, for the first time the X-ray structures of linear M1-linked tri- and tetra-Ubs and a K11/K63-branched tri-Ub.

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Organizational Affiliation: 
• Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.28 kDa 
• Atom Count: 2,745 
• Modeled Residue Count: 304 
• Deposited Residue Count: 304 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A, B	76	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ubiquitin	C, D	76	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens) Explore P62987  Go to UniProtKB:  P62987
PHAROS:  P62987 GTEx:  ENSG00000221983

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  17 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL	C, D	D-PEPTIDE LINKING	C3 H7 N O2		Not Available
DAR	C, D	D-PEPTIDE LINKING	C6 H15 N4 O2		Not Available
DAS	C, D	D-PEPTIDE LINKING	C4 H7 N O4		Not Available
DGL	C, D	D-PEPTIDE LINKING	C5 H9 N O4		Not Available
DGN	C, D	D-PEPTIDE LINKING	C5 H10 N2 O3		Not Available
DHI	C, D	D-PEPTIDE LINKING	C6 H10 N3 O2		Not Available
DIL	C, D	D-PEPTIDE LINKING	C6 H13 N O2		Not Available
DLE	C, D	D-PEPTIDE LINKING	C6 H13 N O2		Not Available
DLY	C, D	D-PEPTIDE LINKING	C6 H14 N2 O2		Not Available
DNE	C, D	D-PEPTIDE LINKING	C6 H13 N O2		Not Available
DPN	C, D	D-PEPTIDE LINKING	C9 H11 N O2		Not Available
DPR	C, D	D-PEPTIDE LINKING	C5 H9 N O2		Not Available
DSG	C, D	D-PEPTIDE LINKING	C4 H8 N2 O3		Not Available
DSN	C, D	D-PEPTIDE LINKING	C3 H7 N O3		Not Available
DTH	C, D	D-PEPTIDE LINKING	C4 H9 N O3		Not Available
DTY	C, D	D-PEPTIDE LINKING	C9 H11 N O3		Not Available
DVA	C, D	D-PEPTIDE LINKING	C5 H11 N O2		Not Available

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.24	α = 98.15
b = 38.26	β = 98.15
c = 48	γ = 109.67

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Gao, S., Pan, M., Zheng, Y.

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Database references
• Version 1.2: 2022-02-09
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection