PDB-3pfm: Crystal structure of a EAL domain of GGDEF domain protein from Ps...

ID or keywords:

Entry

Database: PDB / ID: 3pfm

Title

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

Components

GGDEF domain protein

Keywords

SIGNALING PROTEIN / PSI2 / MCSG /

Structural Genomics /

Protein Structure Initiative / Midwest Center for Structural Genomics /

EAL domain

Function / homology

Function and homology information

membrane => GO:0016020 /

signal transduction
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.908 Å

Authors

Nocek, B. / Stein, A. / Marshall, N. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of a EAL domain of GGDEF domain protein from Pseudomonas fluorescens Pf
Authors: Nocek, B. / Stein, A. / Marshall, N. / Clancy, S. / Joachimiak, A.

History

Deposition	Oct 28, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 10, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.name / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3pfm.cif.gz	107.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3pfm.ent.gz	90.5 KB	Display	PDB format
PDBx/mmJSON format	3pfm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pf/3pfm ftp://data.pdbj.org/pub/pdb/validation_reports/pf/3pfm	HTTPS FTP

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Related structure data

Similar structure data	6y7t-3 4bgo-d 3a7h-3 2jep-d 2z26-d 4e2e-2 6faw-1 5wfx-d 6fav-1 4acz-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: apc38398.2

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#158 - Feb 2013 Proton-Gated Urea Channel similarity (4) #190 - Oct 2015 Two-component Systems similarity (4) #251 - Nov 2020 Adenylyl Cyclase similarity (1) #133 - Jan 2011 Nitric Oxide Synthase similarity (1) #58 - Oct 2004 G Proteins similarity (1)

Deposited unit

A: GGDEF domain protein

28.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GGDEF domain protein

defined by software
56.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.657, 107.861, 159.046
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	24
Space group name H-M	I2₁2₁2₁

#1: Protein	GGDEF domain protein / Mass: 28092.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf-5 / Gene: PFL_0131 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q4KKF5
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 6 Å³/Da / Density % sol: 79.51 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 3.0 M NaCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2010 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.9→40 Å / Num. all: 15103 / Num. obs: 15097 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / R_merge(I) obs: 0.08 / Net I/σ(I): 37
Reflection shell	Resolution: 2.9→3 Å / Redundancy: 7.4 % / R_merge(I) obs: 0.67 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1436 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
Auto-Rickshaw		phasing
HKL-3000		phasing
PHENIX	(phenix.refine: 1.5_2)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.908→40 Å / SU ML: 0.38 / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.237	703	4.99 %	RANDOM
R_work	0.1875	-	-	-
all	0.195	14805	-	-
obs	0.1898	14102	92.5 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 71.62 Å² / k_sol: 0.329 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	50.7549 Å²	-0 Å²	-0 Å²
2-	-	-15.0563 Å²	0 Å²
3-	-	-	-35.6985 Å²

Refinement step

Cycle: LAST / Resolution: 2.908→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1868	0	0	3	1871

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1908
X-RAY DIFFRACTION	f_angle_d	1.149	2593
X-RAY DIFFRACTION	f_dihedral_angle_d	21.623	674
X-RAY DIFFRACTION	f_chiral_restr	0.072	296
X-RAY DIFFRACTION	f_plane_restr	0.004	336

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.9082-3.1326	0.3826	119	0.3135	2226	X-RAY DIFFRACTION	79
3.1326-3.4478	0.2839	155	0.2398	2595	X-RAY DIFFRACTION	91
3.4478-3.9464	0.2462	142	0.1738	2739	X-RAY DIFFRACTION	96
3.9464-4.971	0.1812	154	0.1442	2859	X-RAY DIFFRACTION	98
4.971-43.9669	0.2244	133	0.1828	2980	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.6631	4.3101	-2.7403	4.2225	-2.5799	7.8552	-2.5661	2.5192	-0.6992	0.6943	0.3083	-2.0789	1.0862	2.1511	1.4328	1.9306	-0.4239	0.1217	1.382	0.0217	0.6609	24.7596	11.0298	83.412
2	2.0067	-0.5525	1.8607	9.6516	-7.0375	5.3063	-2.5289	-1.9118	-2.9873	1.1974	2.5255	-0.1189	-1.2246	0.2969	-0.3295	1.4961	0.0245	-0.1592	1.3784	0.2128	0.4193	23.6961	5.7141	78.4591
3	2.043	-0.6737	-0.3913	2.7727	-0.1063	1.5884	-0.1429	-0.6363	-0.06	1.1394	0.4501	0.4646	0.1249	-1.1407	-0.2001	1.0712	-0.1459	0.0622	0.9516	-0.006	0.7382	21.6249	0.6543	66.2331
4	6.7871	-1.3741	5.9225	6.5113	-4.8997	9.8171	-0.6676	-0.7507	0.0198	0.3958	0.7007	0.4663	-1.7203	-0.6422	0.5113	0.4018	-0.2532	-0.0606	0.4241	0.0623	0.677	20.5997	12.1965	41.3306
5	2.2764	-0.5761	1.2363	-0.3856	-0.2346	1.3143	-0.0868	-0.5455	0.2523	0.263	0.039	0.1888	0.5681	-1.0832	0.2636	0.7897	0.0155	-0.0103	0.8538	-0.0986	0.5107	18.4239	7.0219	53.0906
6	3.2816	-2.7394	-2.5811	4.0108	2.746	2.2927	1.0199	-1.3199	1.1648	0.8131	-0.8648	1.4805	1.2651	-4.1741	-0.9856	1.026	-0.0731	-0.0778	1.8519	0.1796	1.1099	12.568	7.8969	67.5412
7	1.5103	1.1949	-0.1472	3.1444	0.8524	0.7466	0.7562	-0.9307	0.3354	1.7307	-0.8668	-0.7137	-1.5024	-0.5134	0.1145	1.414	-0.0511	0.0051	1.0277	0.1208	0.4936	28.7891	9.4586	71.0747
8	0.9344	-0.0202	2.2459	0.8986	1.1169	6.6143	-0.153	0.0264	-1.4036	-0.1801	-0.6127	-0.0108	-0.199	-0.3251	0.1855	1.1614	0.0539	0.1662	0.855	0.1355	0.7642	29.5646	0.5731	64.5949
9	5.334	2.3283	5.7762	4.3808	4.4892	7.6493	-0.1216	-0.6924	-0.1864	-0.8213	-1.1015	0.8272	-0.6333	-0.176	0.7868	0.6269	0.0348	0.0918	0.7791	-0.0602	0.8919	25.8486	-4.621	55.6379
10	3.3814	2.3249	-0.4288	5.5523	2.2661	1.7855	-0.0408	-1.537	0.526	-1.0556	-0.9398	1.0229	-0.4154	-1.2259	0.3464	1.0997	0.108	0.1948	0.6945	0.0276	0.629	25.3333	-0.5146	50.0828
11	2.5095	0.1973	-0.6513	0.2355	-0.8374	6.8248	0.1112	0.0396	-0.4024	0.4855	0.0729	-0.5064	0.7955	-0.2871	0.0938	0.8189	0.0506	-0.1518	0.5561	0.1002	0.555	36.5363	-0.0647	56.2571
12	8.2247	-0.6156	2.847	5.1859	-2.1525	1.7356	1.267	-1.5086	-2.2645	0.4503	-1.4903	-0.098	-0.3605	0.2749	0.5324	0.9945	-0.1127	0.3465	1.3728	0.2296	1.031	45.2672	10.9204	55.8795
13	3.4021	-3.2774	0.6337	7.5584	2.859	3.1643	0.386	-1.0341	-0.6412	0.8635	0.8674	-1.1618	1.2165	2.3598	-0.4401	0.717	0.1024	0.3508	1	-0.0253	0.9752	43.9808	0.0657	50.4687
14	0.6401	-1.8416	0.2846	4.8458	0.3289	3.0737	0.4449	-0.5674	0.2317	2.6936	-0.3957	-1.8516	-0.2858	-0.7541	-0.0234	0.9085	0.2631	-0.0141	0.6478	0.0686	1.0819	36.0775	14.3714	50.5455
15	5.2102	3.3725	-2.8658	9.2361	3.1267	5.068	0.8587	-0.4359	1.6512	1.8092	-2.1998	2.5238	0.884	-0.2915	0.8977	0.8512	0.2105	0.4169	1.1912	-0.0806	0.8748	43.9351	16.8453	46.8151
16	2.937	3.0467	1.1082	2.969	1.0405	0.2297	0.4208	-0.8885	-0.4058	-1.0258	-0.2018	1.2077	-0.3161	-0.7203	0.058	0.7075	0.1687	0.0046	0.7954	-0.0868	0.7512	33.4909	15.7637	47.8625
17	5.3134	2.7166	0.8085	1.4854	-0.4595	5.0863	-1.1581	0.5443	1.3748	0.066	-0.2425	0.1096	-1.6188	0.19	0.6509	0.9575	0.1577	-0.1681	0.6495	-0.1333	0.9377	28.2453	28.2967	43.8568
18	6.1614	-2.3648	0.3374	7.0949	-0.1414	0.0113	-0.9632	0.5036	-1.2739	-4.9506	-2.2758	-1.8851	-0.1674	-0.9209	2.3902	1.3166	0.2061	0.2857	0.6342	0.0228	1.2466	38.5362	15.2698	37.2591
19	5.5969	-1.379	-0.8445	4.0508	2.3307	1.3111	-0.05	-0.0552	0.6396	-0.9821	0.1357	0.6247	-0.9975	-0.4397	0.0813	0.9499	0.1931	-0.098	0.7418	-0.0448	0.9057	22.551	21.1945	42.976
20	1.4688	0.9638	-0.6376	3.0178	-0.2339	0.2163	0.3535	0.1785	0.5205	-1.7399	-0.1558	0.0708	1.2045	-0.7714	0.1964	0.7717	0.0119	0.0182	0.6024	-0.055	0.7706	17.7709	10.3689	49.176

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 407:411)
2	X-RAY DIFFRACTION	2	(chain A and resid 412:416)
3	X-RAY DIFFRACTION	3	(chain A and resid 417:431)
4	X-RAY DIFFRACTION	4	(chain A and resid 432:437)
5	X-RAY DIFFRACTION	5	(chain A and resid 438:454)
6	X-RAY DIFFRACTION	6	(chain A and resid 455:460)
7	X-RAY DIFFRACTION	7	(chain A and resid 461:475)
8	X-RAY DIFFRACTION	8	(chain A and resid 476:481)
9	X-RAY DIFFRACTION	9	(chain A and resid 482:489)
10	X-RAY DIFFRACTION	10	(chain A and resid 490:500)
11	X-RAY DIFFRACTION	11	(chain A and resid 501:535)
12	X-RAY DIFFRACTION	12	(chain A and resid 536:544)
13	X-RAY DIFFRACTION	13	(chain A and resid 545:554)
14	X-RAY DIFFRACTION	14	(chain A and resid 555:567)
15	X-RAY DIFFRACTION	15	(chain A and resid 568:573)
16	X-RAY DIFFRACTION	16	(chain A and resid 574:586)
17	X-RAY DIFFRACTION	17	(chain A and resid 587:607)
18	X-RAY DIFFRACTION	18	(chain A and resid 608:612)
19	X-RAY DIFFRACTION	19	(chain A and resid 613:633)
20	X-RAY DIFFRACTION	20	(chain A and resid 634:648)

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