PDB-8u0i: Crystal structure of PA0012 complexed with cyclic-di-GMP from Pse...

ID or keywords:

Entry

Database: PDB / ID: 8u0i

Title

Crystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa

Components

PilZ domain-containing protein

Keywords

SIGNALING PROTEIN / Complex

Function / homology

PilZ domain / PilZ domain / cyclic-di-GMP binding / Chem-C2E / PilZ domain-containing protein

Function and homology information

Biological species

Pseudomonas aeruginosa PA14 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.541 Å

Authors

Hammons, N.A. / Schnicker, N.J. / Fuentes, E.J.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa
Authors: Hammons, N.A. / Schnicker, N.J. / Fuentes, E.J.

History

Deposition	Aug 29, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 4, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8u0i.cif.gz	55.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8u0i.ent.gz	38.5 KB	Display	PDB format
PDBx/mmJSON format	8u0i.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/u0/8u0i ftp://data.pdbj.org/pub/pdb/validation_reports/u0/8u0i	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (2) #130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: PilZ domain-containing protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	50.317, 50.317, 90.596
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-216- HOH

#1: Protein	PilZ domain-containing protein Mass: 9969.399 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: PA0012 / Plasmid: pET21a Details (production host): Modified with an N-terminal cleavable hexa-His tag Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): K-12 / References: UniProt: Q9I7B4
#2: Chemical	ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.38 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 5.3 mg/mL PA0012 and 2.5 mM cyclic-di-GMP. 0.2 M NH4SO4, 15% (w/v) PEG4000, 0.1 M Tri-NaCit pH=5.6

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0004 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 2, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0004 Å / Relative weight: 1
Reflection	Resolution: 1.54→43.99 Å / Num. obs: 17945 / % possible obs: 100 % / Redundancy: 39.2 % / B_iso Wilson estimate: 23.1 Å² / CC_1/2: 1 / R_merge(I) obs: 0.081 / R_pim(I) all: 0.013 / R_rim(I) all: 0.083 / Χ²: 0.27 / Net I/σ(I): 19
Reflection shell	Resolution: 1.54→1.57 Å / Redundancy: 32.9 % / R_merge(I) obs: 1.064 / Num. unique obs: 865 / CC_1/2: 0.971 / R_pim(I) all: 0.187 / R_rim(I) all: 1.08 / Χ²: 0.01 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
Aimless		data scaling
DIALS		data reduction
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.541→43.988 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.957 / WR_factor R_free: 0.189 / WR_factor R_work: 0.155 / SU B: 1.612 / SU ML: 0.055 / Average fsc free: 0.9656 / Average fsc work: 0.9708 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2101	873	4.881 %	RANDOM
R_work	0.1733	17012	-	-
all	0.175	-	-	-
obs	-	17885	99.989 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.158 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.631 Å²	0 Å²	-0 Å²
2-	-	0.631 Å²	-0 Å²
3-	-	-	-1.262 Å²

Refinement step

Cycle: LAST / Resolution: 1.541→43.988 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	663	0	110	91	864

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	803
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	721
X-RAY DIFFRACTION	r_angle_refined_deg	2.048	1.837	1115
X-RAY DIFFRACTION	r_angle_other_deg	0.744	1.747	1672
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.885	5	90
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.335	5	6
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.516	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.457	10	118
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.98	10	29
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	134
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	866
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	162
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	119
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	734
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	387
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.093	0.2	470
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.174	0.2	62
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.228	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.211	0.2	45
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.087	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	2.629	2.425	346
X-RAY DIFFRACTION	r_mcbond_other	2.628	2.418	345
X-RAY DIFFRACTION	r_mcangle_it	3.931	4.319	433
X-RAY DIFFRACTION	r_mcangle_other	3.928	4.318	433
X-RAY DIFFRACTION	r_scbond_it	3.889	2.806	457
X-RAY DIFFRACTION	r_scbond_other	3.89	2.808	458
X-RAY DIFFRACTION	r_scangle_it	5.714	4.929	679
X-RAY DIFFRACTION	r_scangle_other	5.709	4.93	680
X-RAY DIFFRACTION	r_lrange_it	6.971	30.04	932
X-RAY DIFFRACTION	r_lrange_other	6.977	30.045	933

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.541-1.581	0.268	51	0.301	1250	0.3	1303	0.908	0.917	99.8465	0.294
1.581-1.624	0.24	69	0.272	1193	0.27	1262	0.963	0.938	100	0.261
1.624-1.671	0.327	58	0.233	1157	0.237	1215	0.932	0.956	100	0.215
1.671-1.723	0.219	44	0.217	1144	0.217	1188	0.961	0.965	100	0.195
1.723-1.779	0.248	66	0.197	1093	0.2	1159	0.964	0.971	100	0.17
1.779-1.841	0.206	53	0.19	1050	0.191	1103	0.976	0.976	100	0.162
1.841-1.911	0.236	49	0.176	1043	0.179	1092	0.968	0.979	100	0.145
1.911-1.989	0.198	55	0.165	1002	0.167	1057	0.976	0.982	100	0.135
1.989-2.077	0.173	46	0.167	948	0.167	994	0.978	0.983	100	0.139
2.077-2.178	0.159	44	0.149	925	0.149	969	0.985	0.987	100	0.126
2.178-2.296	0.184	49	0.158	888	0.159	937	0.98	0.986	100	0.133
2.296-2.434	0.243	40	0.154	813	0.158	853	0.966	0.984	100	0.129
2.434-2.602	0.193	46	0.171	787	0.172	833	0.978	0.982	100	0.143
2.602-2.81	0.233	51	0.173	736	0.177	787	0.968	0.981	100	0.144
2.81-3.076	0.25	38	0.168	669	0.172	707	0.96	0.982	100	0.144
3.076-3.437	0.207	28	0.163	630	0.164	658	0.978	0.984	100	0.146
3.437-3.965	0.168	31	0.143	561	0.144	592	0.984	0.988	100	0.135
3.965-4.847	0.212	25	0.141	482	0.144	507	0.976	0.989	100	0.136
4.847-6.813	0.23	17	0.208	391	0.209	408	0.982	0.981	100	0.198
6.813-43.988	0.186	13	0.229	250	0.227	263	0.973	0.972	100	0.228

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