PDB-8v7p: Crystal structure of the truncated P1 pilin from Pseudomonas aeru...

ID or keywords:

Entry

Database: PDB / ID: 8v7p

Title

Crystal structure of the truncated P1 pilin from Pseudomonas aeruginosa

Components

Fimbrial protein

Keywords

CELL ADHESION / Pilin protein / Fimbrial protein / Pseudomonas aeruginosa

Function / homology

Function and homology information

protein secretion by the type II secretion system / type II protein secretion system complex / pilus / cell adhesion / membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Authors

Bragagnolo, N.J. / Audette, G.F.

Funding support

Canada, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2024
Title: The 1.3 angstrom resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1.
Authors: Bragagnolo, N. / Audette, G.F.

History

Deposition	Dec 4, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2024	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8v7p.cif.gz	91.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8v7p.ent.gz	52 KB	Display	PDB format
PDBx/mmJSON format	8v7p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8v7p_validation.pdf.gz	430.3 KB	Display	wwPDB validaton report
Full document	8v7p_full_validation.pdf.gz	431.3 KB	Display
Data in XML	8v7p_validation.xml.gz	11 KB	Display
Data in CIF	8v7p_validation.cif.gz	15.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v7/8v7p ftp://data.pdbj.org/pub/pdb/validation_reports/v7/8v7p	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	#211 - Jul 2017 Pilus Machine similarity (5)

Deposited unit

A: Fimbrial protein

hetero molecules

13.2 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)	22.453, 54.853, 37.772
Angle α, β, γ (deg.)	90.000, 96.145, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Fimbrial protein Mass: 13049.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: P1 / Gene: pilA / Plasmid: pMAL-p2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2507 / References: UniProt: P17836
#2: Chemical	ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE Mass: 137.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₇AsO₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 1.77 Å³/Da / Density % sol: 30.72 % / Description: Rod-like
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 35% PEG8000, 100 mM sodium cacodylate, 200 mM sodium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.3.1 / Wavelength: 1.0236 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 4, 2003

Radiation

Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0236 Å / Relative weight: 1

Reflection

Resolution: 0.94→54.9 Å / Num. obs: 22344 / % possible obs: 99.5 % / Redundancy: 4 % / B_iso Wilson estimate: 10.5 Å² / CC_1/2: 0.988 / R_merge(I) obs: 0.141 / R_pim(I) all: 0.069 / R_rim(I) all: 0.158 / Χ²: 1.96 / Net I/σ(I): 14.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
6.5-54.85	3.9	0.07	28.7	196	0.998	0.042	0.083	2.29	99.4
1.3-1.33	2.7	0.498	3.9	1309	0.639	0.355	0.615	1.39	99.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
MOSFLM		data reduction
Aimless	0.7.13	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.3→37.555 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.96 / SU B: 2.066 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.053
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1738	682	3.055 %	Random
R_work	0.1306	21642	-	-
all	0.132	-	-	-
obs	-	22324	99.492 %	-

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: 10.936 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.134 Å²	-0 Å²	0.209 Å²
2-	-	0.33 Å²	0 Å²
3-	-	-	-0.236 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→37.555 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	915	0	5	216	1136

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	983
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	963
X-RAY DIFFRACTION	r_angle_refined_deg	1.916	1.823	1349
X-RAY DIFFRACTION	r_angle_other_deg	0.664	1.782	2249
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.917	5	140
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.78	5	3
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.033	10	180
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.375	10	33
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	164
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1145
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	191
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	206
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.21	0.2	887
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	494
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	513
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.261	0.2	127
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.167	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.19	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.269	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.189	0.2	50
X-RAY DIFFRACTION	r_mcbond_it	3.201	0.983	513
X-RAY DIFFRACTION	r_mcbond_other	3.199	0.983	513
X-RAY DIFFRACTION	r_mcangle_it	4.7	1.767	644
X-RAY DIFFRACTION	r_mcangle_other	4.697	1.768	645
X-RAY DIFFRACTION	r_scbond_it	4.751	1.249	470
X-RAY DIFFRACTION	r_scbond_other	4.746	1.25	471
X-RAY DIFFRACTION	r_scangle_it	6.883	2.184	696
X-RAY DIFFRACTION	r_scangle_other	6.878	2.184	697
X-RAY DIFFRACTION	r_lrange_it	15.118	22.853	1240
X-RAY DIFFRACTION	r_lrange_other	13.032	16.645	1182
X-RAY DIFFRACTION	r_rigid_bond_restr	3.812	3	1946

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
1.3-1.334	0.29	39	0.25	1603	0.251	1653	0.947	0.959	99.3345	0.209
1.334-1.37	0.34	43	0.225	1532	0.228	1591	0.802	0.967	98.9943	0.187
1.37-1.41	0.177	40	0.18	1543	0.18	1591	0.982	0.976	99.4972	0.149
1.41-1.453	0.171	36	0.135	1449	0.136	1497	0.981	0.988	99.1984	0.104
1.453-1.501	0.169	42	0.125	1454	0.127	1509	0.975	0.989	99.1385	0.101
1.501-1.553	0.152	31	0.132	1354	0.132	1405	0.985	0.986	98.5765	0.107
1.553-1.612	0.151	43	0.119	1328	0.12	1381	0.985	0.99	99.2759	0.101
1.612-1.678	0.199	48	0.12	1240	0.122	1304	0.972	0.99	98.773	0.106
1.678-1.752	0.195	47	0.123	1237	0.126	1290	0.98	0.989	99.5349	0.111
1.752-1.837	0.193	41	0.113	1176	0.116	1217	0.975	0.992	100	0.108
1.837-1.937	0.129	31	0.105	1110	0.106	1141	0.989	0.993	100	0.102
1.937-2.054	0.127	47	0.106	1066	0.107	1113	0.989	0.993	100	0.104
2.054-2.195	0.159	38	0.113	989	0.115	1027	0.985	0.993	100	0.12
2.195-2.37	0.154	38	0.114	929	0.115	967	0.988	0.992	100	0.119
2.37-2.595	0.185	30	0.118	850	0.12	880	0.98	0.991	100	0.128
2.595-2.9	0.155	31	0.12	775	0.122	806	0.987	0.991	100	0.144
2.9-3.345	0.142	21	0.122	689	0.123	711	0.987	0.99	99.8594	0.143
3.345-4.089	0.208	15	0.113	588	0.115	603	0.977	0.992	100	0.139
4.089-5.749	0.208	11	0.148	469	0.15	480	0.981	0.99	100	0.181
5.749-37.555	0.251	10	0.225	260	0.226	271	0.96	0.98	99.631	0.3

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