4A27 | pdb_00004a27

Crystal structure of human synaptic vesicle membrane protein VAT-1 homolog-like protein

• PDB DOI: https://doi.org/10.2210/pdb4A27/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-22 Released: 2011-10-19 
• Deposition Author(s): Vollmar, M., Shafqat, N., Muniz, J.R.C., Krojer, T., Allerston, C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Yue, W.W., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.230 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Synaptic Vesicle Membrane Protein Vat-1 Homolog-Like Protein

Vollmar, M., Shafqat, N., Muniz, J.R.C., Krojer, T., Allerston, C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Yue, W.W., Oppermann, U.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.35 kDa 
• Atom Count: 4,862 
• Modeled Residue Count: 623 
• Deposited Residue Count: 698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNAPTIC VESICLE MEMBRANE PROTEIN VAT-1 HOMOLOG-LIKE	A, B	349	Homo sapiens	Mutation(s): 0  EC: 1 (PDB Primary Data), 1.6.5.5 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCJ6 (Homo sapiens) Explore Q9HCJ6  Go to UniProtKB:  Q9HCJ6
PHAROS:  Q9HCJ6 GTEx:  ENSG00000171724

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.230 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.509	α = 90
b = 62.104	β = 106.98
c = 83.795	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-19 
Deposition Author(s): Vollmar, M., Shafqat, N., Muniz, J.R.C., Krojer, T., Allerston, C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Yue, W.W., Oppermann, U.

Revision History  

• Version 1.0: 2011-10-19
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description