5HYB | pdb_00005hyb

Crystal structure of myristoylated Y81A mutant MMTV matrix protein

• PDB DOI: https://doi.org/10.2210/pdb5HYB/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Mouse mammary tumor virus (STRAIN BR6)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-02-01 Released: 2017-06-28 
• Deposition Author(s): Brynda, J., Dostal, J., Zabransky, A., Dolezal, M.
• Funding Organization(s): Czech Science Foundation (GA CR), NPU, RVO

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.274 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of myristoylated Y81A mutant MMTV matrix protein

Brynda, J., Dostal, J., Zabransky, A., Dolezal, M.

To be published.

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  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.46 kDa 
• Atom Count: 1,636 
• Modeled Residue Count: 182 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix Protein	A, B	91	Mouse mammary tumor virus (STRAIN BR6)	Mutation(s): 1  Gene Names: gag
UniProt
Find proteins for P10258 (Mouse mammary tumor virus (strain BR6)) Explore P10258  Go to UniProtKB:  P10258

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYR	C [auth A], E [auth B]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
PEG	D [auth A], F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.274 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.802	α = 90
b = 61.802	β = 90
c = 89.622	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Brynda, J., Dostal, J., Zabransky, A., Dolezal, M.

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Funding Organization	Location	Grant Number
Czech Science Foundation (GA CR)	Czech Republic	15-05677S
NPU	Czech Republic	LO1302
NPU	Czech Republic	LO1304
RVO	Czech Republic	RVO 61388963
RVO	Czech Republic	RVO 68378050
RVO	Czech Republic	RVO: 68378050

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary