7AC6 | pdb_00007ac6

Structure of sponge-phase grown PepTst2 collected by rotation serial crystallography on a COC membrane at a synchrotron source


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.287 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7AC6

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Versatile microporous polymer-based supports for serial macromolecular crystallography.

Martiel, I.Beale, J.H.Karpik, A.Huang, C.Y.Vera, L.Olieric, N.Wranik, M.Tsai, C.J.Muhle, J.Aurelius, O.John, J.Hogbom, M.Wang, M.Marsh, M.Padeste, C.

(2021) Acta Crystallogr D Struct Biol 77: 1153-1167

  • DOI: https://doi.org/10.1107/S2059798321007324
  • Primary Citation Related Structures: 
    7AC2, 7AC3, 7AC4, 7AC5, 7AC6, 7AI8, 7AI9

  • PubMed Abstract: 

    Serial data collection has emerged as a major tool for data collection at state-of-the-art light sources, such as microfocus beamlines at synchrotrons and X-ray free-electron lasers. Challenging targets, characterized by small crystal sizes, weak diffraction and stringent dose limits, benefit most from these methods. Here, the use of a thin support made of a polymer-based membrane for performing serial data collection or screening experiments is demonstrated. It is shown that these supports are suitable for a wide range of protein crystals suspended in liquids. The supports have also proved to be applicable to challenging cases such as membrane proteins growing in the sponge phase. The sample-deposition method is simple and robust, as well as flexible and adaptable to a variety of cases. It results in an optimally thin specimen providing low background while maintaining minute amounts of mother liquor around the crystals. The 2 × 2 mm area enables the deposition of up to several microlitres of liquid. Imaging and visualization of the crystals are straightforward on the highly transparent membrane. Thanks to their affordable fabrication, these supports have the potential to become an attractive option for serial experiments at synchrotrons and free-electron lasers.


  • Organizational Affiliation
    • Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 58.81 kDa 
  • Atom Count: 3,976 
  • Modeled Residue Count: 455 
  • Deposited Residue Count: 480 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Di-or tripeptide:H+ symporter478Streptococcus thermophilus LMG 18311Mutation(s): 0 
Gene Names: dtpTstu0970
Membrane Entity: Yes 
UniProt
Find proteins for Q5M4H8 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311))
Explore Q5M4H8 
Go to UniProtKB:  Q5M4H8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5M4H8
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Di-or tripeptide:H+ symporterB [auth Y]2Streptococcus thermophilus LMG 18311Mutation(s): 0 
Gene Names: dtpTstu0970

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
78M

Query on 78M



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
C18 H34 O4
BJMLBVHMHXYQFS-JJEJIETFSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
X [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PG0

Query on PG0



Download:Ideal Coordinates CCD File
W [auth A]2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.287 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.76α = 90
b = 110.23β = 90
c = 109.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description