5NYV

Crystal structure determination from picosecond infrared laser ablated protein crystals by serial synchrotron crystallography

• PDB DOI: https://doi.org/10.2210/pdb5NYV/pdb

• Classification: HYDROLASE
• Organism(s): Rhodopseudomonas palustris ATCC 17001
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-11 Released: 2018-03-21 
• Deposition Author(s): Schulz, E.C., Kaub, J., Busse, F., Mehrabi, P., Mueller-Werkmeiser, H., Pai, E.F., Robertson, W.D., Miller, R.J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Protein crystals IR laser ablated from aqueous solution at high speed retain their diffractive properties: applications in high-speed serial crystallography.

Schulz, E.C., Kaub, J., Busse, F., Mehrabi, P., Muller-Werkmeister, H.M., Pai, E.F., Robertson, W.D., Miller, R.J.D.

(2017) J Appl Crystallogr 50: 1773-1781

• DOI: https://doi.org/10.1107/S1600576717014479

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: 68.15 kDa 
• Atom Count: 5,108 
• Modelled Residue Count: 594 
• 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 ATCC 17001	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.535	α = 90
b = 80.889	β = 102.72
c = 85.633	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction
cctbx.prime	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Schulz, E.C., Kaub, J., Busse, F., Mehrabi, P., Mueller-Werkmeiser, H., Pai, E.F., Robertson, W.D., Miller, R.J.D.

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references