5NYV | pdb_00005nyv

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.219 (Depositor), 0.218 (DCC)
R-Value Work:
0.193 (Depositor), 0.192 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5NYV

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 68.15 kDa
Atom Count: 5,108
Modeled Residue Count: 594
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NAM1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.219 (Depositor), 0.218 (DCC)
R-Value Work: 0.193 (Depositor), 0.192 (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

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Entry History

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Mueller-Werkmeiser, H.

Robertson, W.D.

Revision History (Full details and data files)

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

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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.