3HVW | pdb_00003hvw

Crystal Structure of the GGDEF domain of the PA2567 protein from Pseudomonas aeruginosa, Northeast Structural Genomics Consortium Target PaR365C

PDB DOI: https://doi.org/10.2210/pdb3HVW/pdb

Classification: LYASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-16 Released: 2009-06-23
Deposition Author(s): Forouhar, F., Lew, S., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Foote, E.L., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.219 (Depositor), 0.223 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target PaR365C

Forouhar, F., Lew, S., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Foote, E.L., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 20.09 kDa
Atom Count: 1,495
Modeled Residue Count: 159
Deposited Residue Count: 176
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diguanylate-cyclase (DGC)	A	176	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: PA2567 EC: 3.1.4.52
UniProt
Find proteins for Q9I0R8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I0R8 Go to UniProtKB: Q9I0R8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I0R8
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: 1.70 Å
R-Value Free: 0.219 (Depositor), 0.223 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.374	α = 90
b = 53.757	β = 90
c = 76.792	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-06-23

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-06-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Structure summary