3PFM | pdb_00003pfm

Crystal structure of a EAL domain of GGDEF domain protein from Pseudomonas fluorescens Pf

PDB DOI: https://doi.org/10.2210/pdb3PFM/pdb

Classification: SIGNALING PROTEIN
Organism(s): Pseudomonas protegens Pf-5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-10-28 Released: 2010-11-10
Deposition Author(s): Nocek, B., Stein, A., Marshall, N., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free:
0.237 (Depositor), 0.234 (DCC)
R-Value Work:
0.188 (Depositor), 0.200 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3PFM

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a EAL domain of GGDEF domain protein from Pseudomonas fluorescens Pf

Nocek, B., Stein, A., Marshall, N., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 28.09 kDa
Atom Count: 1,871
Modeled Residue Count: 243
Deposited Residue Count: 243
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GGDEF domain protein	A	243	Pseudomonas protegens Pf-5	Mutation(s): 0 Gene Names: PFL_0131
UniProt
Find proteins for Q4KKF5 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4KKF5 Go to UniProtKB: Q4KKF5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4KKF5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.237 (Depositor), 0.234 (DCC)
R-Value Work: 0.188 (Depositor), 0.200 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.657	α = 90
b = 107.861	β = 90
c = 159.046	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
Auto-Rickshaw	phasing
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-11-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.