7TCV | pdb_00007tcv

VDAC K12E mutant

PDB DOI: https://doi.org/10.2210/pdb7TCV/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli M15
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2021-12-28 Released: 2023-01-11
Deposition Author(s): Khan, F., Abramson, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.277 (Depositor), 0.279 (DCC)
R-Value Work:
0.217 (Depositor), 0.219 (DCC)

Starting Model: experimental
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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

Dynamical control of the mitochondrial beta-barrel channel VDAC by electrostatic and mechanical coupling

Ngo, V.A., Martin, M.Q., Khan, F., Bergdoll, L., Abramson, J., Bezrukov, S.M., Rostovtseva, T.K., Hoogerheide, D.P., Noskov, S.Y.

To be published.

Macromolecule Content

Total Structure Weight: 32.87 kDa
Atom Count: 2,172
Modeled Residue Count: 283
Deposited Residue Count: 295
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent anion-selective channel protein 1	A [auth XXX]	295	Mus musculus	Mutation(s): 1 Gene Names: Vdac1, Vdac5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q60932 (Mus musculus) Explore Q60932 Go to UniProtKB: Q60932
IMPC: MGI:106919
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60932
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MC3 Query on MC3 Download:Ideal Coordinates CCD File SDF format, chain B [auth XXX] MOL2 format, chain B [auth XXX] mmCIF format, chain B [auth XXX]	B [auth XXX]	1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE C₃₆ H₇₂ N O₈ P CITHEXJVPOWHKC-UUWRZZSWSA-N		Interactions Focus chain B [auth XXX] Interactions & Density Focus chain B [auth XXX]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.277 (Depositor), 0.279 (DCC)
R-Value Work: 0.217 (Depositor), 0.219 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.197	α = 90
b = 57.8	β = 97.664
c = 66.44	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-01-11
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.