6GXT

The hit-and-return system enables efficient time-resolved serial synchrotron crystallography: FAcD2052MS after reaction initiation

• PDB DOI: https://doi.org/10.2210/pdb6GXT/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Rhodopseudomonas palustris CGA009
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-27 Released: 2018-10-17 
• Deposition Author(s): Schulz, E.C., Mehrabi, P., Mueller-Werkmeister, H., Tellkamp, F., Stuart, W., Persch, E., De Gasparo, R., Diederich, F., Pai, E.F., Miller, R.J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.228 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Literature

The hit-and-return system enables efficient time-resolved serial synchrotron crystallography.

Schulz, E.C., Mehrabi, P., Muller-Werkmeister, H.M., Tellkamp, F., Jha, A., Stuart, W., Persch, E., De Gasparo, R., Diederich, F., Pai, E.F., Miller, R.J.D.

(2018) Nat Methods 15: 901-904

• PubMed: 30377366 
• DOI: https://doi.org/10.1038/s41592-018-0180-2
• Primary Citation of Related Structures:  
  6FSX, 6GXD, 6GXF, 6GXH, 6GXL, 6GXT


• PubMed Abstract: 
  

  We present a 'hit-and-return' (HARE) method for time-resolved serial synchrotron crystallography with time resolution from milliseconds to seconds or longer. Timing delays are set mechanically, using the regular pattern in fixed-target crystallography chips and a translation stage system. Optical pump-probe experiments to capture intermediate structures of fluoroacetate dehalogenase binding to its ligand demonstrated that data can be collected at short (30 ms), medium (752 ms) and long (2,052 ms) intervals.

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Organizational Affiliation: 

Department for Atomically Resolved Dynamics, Max Planck Institute for Structure and Dynamics of Matter, Hamburg, Germany.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 68.23 kDa 
• Atom Count: 4,952 
• Modelled Residue Count: 595 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluoroacetate dehalogenase	A, B	306	Rhodopseudomonas palustris CGA009	Mutation(s): 0  Gene Names: RPA1163 EC: 3.8.1.3
UniProt
Find proteins for Q6NAM1 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NAM1  Go to UniProtKB:  Q6NAM1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAH (Subject of Investigation/LOI)	C [auth A]	fluoroacetic acid C2 H3 F O2 QEWYKACRFQMRMB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.228 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.76	α = 90
b = 79.54	β = 102.94
c = 84.46	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Schulz, E.C., Mehrabi, P., Mueller-Werkmeister, H., Tellkamp, F., Stuart, W., Persch, E., De Gasparo, R., Diederich, F., Pai, E.F., Miller, R.J.D.

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2018-11-14
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description