7SIQ

Crystal structure of a peptide chain release factor 3 (prfC) from Stenotrophomonas maltophilia bound to GDP

PDB DOI: https://doi.org/10.2210/pdb7SIQ/pdb

Classification: HYDROLASE
Organism(s): Stenotrophomonas maltophilia K279a
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-10-14 Released: 2021-10-27
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.279
R-Value Work: 0.224
R-Value Observed: 0.226

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a peptide chain release factor 3 (prfC) from Stenotrophomonas maltophilia bound to GDP

Edwards, T.E., Abendroth, J., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease

To be published.

Macromolecule Content

Total Structure Weight: 60.49 kDa
Atom Count: 3,899
Modelled Residue Count: 524
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide chain release factor 3	A	542	Stenotrophomonas maltophilia K279a	Mutation(s): 0 Gene Names: prfC, Smlt3637
UniProt
Find proteins for B2FR00 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FR00 Go to UniProtKB: B2FR00
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2FR00
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.279
R-Value Work: 0.224
R-Value Observed: 0.226
Space Group: P 3₂ 2 1
Diffraction Data: https://doi.org/10.18430/M37SIQ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.54	α = 90
b = 96.54	β = 90
c = 170.07	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-27

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-10-27
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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.