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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.274 (Depositor), 0.267 (DCC)
R-Value Work:
0.212 (Depositor), 0.216 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of myristoylated Y81A mutant MMTV matrix protein

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

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10258
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYR Query on MYR 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] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
PEG Query on PEG 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] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-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: 1.94 Å
R-Value Free: 0.274 (Depositor), 0.267 (DCC)
R-Value Work: 0.212 (Depositor), 0.216 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-06-28

Deposition Author(s):

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 (Full details and data files)

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

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