PDB-3wpr: Acinetobacter sp. Tol 5 AtaA N-terminal half of C-terminal stalk ...

ID or keywords:

Entry

Database: PDB / ID: 3wpr

Title

Acinetobacter sp. Tol 5 AtaA N-terminal half of C-terminal stalk fused to GCN4 adaptors (CstalkN)

Components

Trimeric autotransporter adhesin

Keywords

CELL ADHESION / adhesin / trimeric autotransporter adhesin / TAA / nanofiber

Function / homology

Function and homology information

cell outer membrane / protein transport / cell adhesion / cell surface
Similarity search - Function

Biological species

Acinetobacter (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.899 Å

Authors

Koiwai, K. / Hartmann, M.D. / Yoshimoto, S. / Nur 'Izzah, N. / Suzuki, A. / Linke, D. / Lupas, A.N. / Hori, K.

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Toughness and Flexibility in the C-terminal Passenger Domain of an Acinetobacter Trimeric Autotransporter Adhesin.
Authors: Koiwai, K. / Hartmann, M.D. / Linke, D. / Lupas, A.N. / Hori, K.

History

Deposition	Jan 15, 2014	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 4, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 30, 2015	Group: Database references
Revision 1.2	Nov 20, 2019	Group: Database references / Category: citation / struct_ref_seq_dif Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.3	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3wpr.cif.gz	251.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3wpr.ent.gz	204.2 KB	Display	PDB format
PDBx/mmJSON format	3wpr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3wpr_validation.pdf.gz	455.3 KB	Display	wwPDB validaton report
Full document	3wpr_full_validation.pdf.gz	460.3 KB	Display
Data in XML	3wpr_validation.xml.gz	25.6 KB	Display
Data in CIF	3wpr_validation.cif.gz	36.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wp/3wpr ftp://data.pdbj.org/pub/pdb/validation_reports/wp/3wpr	HTTPS FTP

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Related structure data

Related structure data	3wp8C 3wpaSC 3wpoC 3wppC 3wqaC 2ynyS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3ok4-d 4cpc-1 4cpc-2 3wqa-d 6qp4-d 5bvz-2 Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Trimeric autotransporter adhesin

B: Trimeric autotransporter adhesin

C: Trimeric autotransporter adhesin

72.8 kDa, 3 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)	71.390, 42.980, 118.070
Angle α, β, γ (deg.)	90.00, 101.01, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Trimeric autotransporter adhesin Mass: 24281.203 Da / Num. of mol.: 3 / Fragment: UNP residues 3170-3332 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter (bacteria) / Strain: Tol 5 / Gene: ataA / Plasmid: pIBA-GCN4tri / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: K7ZP88
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Trimeric autotransporter adhesin

Mass: 24281.203 Da / Num. of mol.: 3 / Fragment: UNP residues 3170-3332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Acinetobacter (bacteria) / Strain: Tol 5 / Gene: ataA / Plasmid: pIBA-GCN4tri / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: K7ZP88

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.44 Å³/Da / Density % sol: 49.61 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.13M Na-acetate, 0.66M Na-citrate, 6.7% PEG 4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2013

Radiation

Monochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.899→38.632 Å / Num. all: 55815 / Num. obs: 55815 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / B_iso Wilson estimate: 31.87 Å²

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.9-2.01		0.92	0.694	1.85	30213	8943	8788	0.823	98.3
2.01-2.15		0.982	0.34	3.45	28656	8509	8468	0.405	99.5
2.15-2.32		0.988	0.226	5.11	25671	7875	7841	0.271	99.6
2.32-2.55		0.996	0.141	7.92	25276	7274	7261	0.167	99.8
2.55-2.84		0.998	0.081	12.8	21869	6576	6562	0.097	99.8
2.84-3.28		0.999	0.043	21.98	19992	5853	5837	0.051	99.7
3.28-4.01		0.999	0.028	35.76	16454	4971	4940	0.033	99.4
4.01-5.64		1	0.018	49.23	12862	3896	3872	0.021	99.4
	5.64	0.999	0.02	54.22	7082	2281	2246	0.024	98.5

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.14	data extraction
XDS		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2YNY, 3WPA

2yny

3wpa

Resolution: 1.899→38.632 Å / FOM work R set: 0.6282 / SU ML: 0.26 / σ(F): 1.35 / Phase error: 40.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2789	2758	4.99 %
R_work	0.2363	-	-
obs	0.2383	55325	98.54 %
all	-	55331	-

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 165.27 Å² / B_iso mean: 65.05 Å² / B_iso min: 32.32 Å²

Refinement step

Cycle: LAST / Resolution: 1.899→38.632 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4606	0	0	263	4869

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4625
X-RAY DIFFRACTION	f_angle_d	0.689	6314
X-RAY DIFFRACTION	f_chiral_restr	0.046	828
X-RAY DIFFRACTION	f_plane_restr	0.002	831
X-RAY DIFFRACTION	f_dihedral_angle_d	12.546	1610

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	Num. reflection all	% reflection obs (%)
1.8992-1.9319	0.5101	131	0.4556	2498	2629	94
1.9319-1.967	0.457	136	0.428	2580	2716	98
1.967-2.0049	0.4597	136	0.4145	2580	2716	99
2.0049-2.0458	0.45	137	0.391	2638	2775	98
2.0458-2.0903	0.4725	134	0.3644	2563	2697	99
2.0903-2.1389	0.3914	138	0.3373	2621	2759	98
2.1389-2.1924	0.361	135	0.3063	2577	2712	98
2.1924-2.2516	0.3337	138	0.2954	2618	2756	99
2.2516-2.3179	0.3604	138	0.2847	2616	2754	99
2.3179-2.3927	0.3253	136	0.2633	2625	2761	99
2.3927-2.4782	0.3005	136	0.2412	2601	2737	99
2.4782-2.5774	0.297	139	0.241	2644	2783	99
2.5774-2.6947	0.3044	140	0.2241	2654	2794	99
2.6947-2.8367	0.2591	137	0.2135	2617	2754	99
2.8367-3.0144	0.2385	140	0.2205	2655	2795	100
3.0144-3.247	0.2852	142	0.2282	2690	2832	100
3.247-3.5736	0.2812	141	0.2134	2679	2820	100
3.5736-4.0902	0.2257	139	0.1991	2653	2792	99
4.0902-5.1512	0.1939	141	0.1756	2696	2837	99
5.1512-38.6404	0.2606	144	0.2279	2762	2906	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	3.3277	-0.1739	-1.4406	1.4236	-0.3455	5.147	-0.4753	-0.7984	-0.754	0.1416	-0.1237	0.0178	0.5562	0.3015	0.5202	0.7763	0.1327	-0.0061	0.5644	0.0897	0.4688	-70.7675	-4.9737	168.7773
2	1.6946	0.1174	-0.379	1.619	-0.1758	2.6722	0.0125	-0.1187	0.1307	-0.2021	-0.1644	-0.3816	-0.8703	0.914	0.0841	0.6447	-0.1494	0.069	0.454	-0.0539	0.4878	-52.9418	6.2028	127.9177
3	1.4399	0.5984	-0.3996	1.0973	-0.6513	0.8018	0.2758	-0.0565	0.1071	0.2426	-0.2206	0.0828	-0.1479	0.1999	-0.0561	0.5632	0.0757	0.0854	0.3316	0.0433	0.5341	-42.9819	-2.2338	86.7333
4	2.5404	-0.1004	-1.6584	2.6049	0.378	3.4165	0.3551	0.2887	0.3088	-0.3986	0.1112	-0.1268	-0.7301	0.2533	-0.39	0.2793	-0.0355	-0.1081	0.5108	0.0532	0.44	-15.4829	2.9772	49.5439
5	2.6515	-0.3329	-1.9873	0.5005	-0.6117	2.9065	0.5782	0.2991	-0.197	-0.1172	-0.5112	-0.2407	-0.7077	0.0963	0.0433	1.1447	0.015	0.2856	1.1333	0.026	0.7072	11.4274	-3.5562	7.2254
6	1.2491	-0.2772	-1.967	0.8166	-0.0743	6.2085	-0.0533	-0.6268	0.0286	0.1735	-0.0418	-0.3148	-1.2817	0.6479	0.1497	0.7267	0.1452	-0.0486	0.6326	-0.0202	0.4835	-69.4034	6.0424	166.9973
7	1.5014	-0.6741	-0.8497	1.7913	0.182	3.4184	-0.3219	0.4459	-0.3132	-0.3037	-0.1778	0.0739	0.3907	-0.6661	0.4182	0.8042	-0.1132	0.2034	0.4471	-0.0832	0.6118	-61.9224	0.1182	123.9687
8	2.1867	-0.1778	-2.0117	1.3509	-0.6865	4.6272	0.1912	-0.7589	0.1343	0.477	-0.1365	0.1696	-0.294	1.2993	-0.042	0.6292	-0.0413	0.0574	0.5731	-0.0315	0.5068	-34.3428	-3.7399	91.0121
9	1.8154	0.4588	-1.0456	1.7597	-0.6446	2.2478	0.1021	0.6916	0.08	-0.315	0.1924	0.2327	-0.2047	-0.4585	-0.2302	0.3202	0.0496	-0.152	0.5873	0.0416	0.4158	-20.3522	0.0845	46.9932
10	0.0474	-0.0629	-0.084	0.3167	0.9148	2.746	-0.2971	0.4325	-0.1581	-0.1841	-0.7238	-1.1041	-0.4283	-0.6771	0.4434	1.0967	-0.0169	0.4954	1.2652	0.081	0.8991	3.5963	5.7638	16.0031
11	2.5037	0.0189	-1.3939	2.1008	-0.2843	5.6386	-0.6428	0.1236	-0.2141	-0.2886	0.1013	0.1954	0.0269	-1.9029	0.2748	0.7569	0.0859	0.0198	0.7312	-0.0365	0.4743	-78.4376	1.0875	165.1074
12	2.4566	0.8164	-0.5265	1.4739	0.274	3.306	-0.4516	-0.5431	-0.7041	0.2714	0.0347	-0.0435	1.1791	0.8882	0.3698	0.9504	0.0593	0.1994	0.5515	-0.0129	0.5916	-53.332	-5.3993	128.3056
13	2.2991	0.0548	-2.203	0.8632	0.1917	3.1561	0.883	-0.3912	0.8173	0.1101	-0.1312	0.2937	-1.2065	0.3647	-0.7417	0.749	-0.1343	0.1974	0.47	-0.0761	0.6083	-37.6083	5.5136	89.3912
14	2.1053	-0.0379	-1.2383	1.439	-0.1083	1.7405	-0.104	0.2017	-0.1188	-0.1873	-0.0172	-0.1973	0.0239	0.1787	0.1192	0.2642	-0.0128	-0.1047	0.5107	0.0137	0.4394	-15.6949	-3.2557	49.3845
15	1.5938	-0.1237	-2.2295	0.1974	0.3012	3.0649	0.5868	0.6244	0.161	-1.1379	-0.3183	0.0926	-0.2573	-0.2381	-0.1716	1.3428	0.3717	0.2216	2.281	0.0996	0.7108	-0.609	-1.5155	5.8491

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESSEQ 3142:3174)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESSEQ 3175:3225)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESSEQ 3226:3262)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESSEQ 3263:3330)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESSEQ 3331:3366)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESSEQ 3144:3174)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESSEQ 3175:3225)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESSEQ 3226:3262)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESSEQ 3263:3330)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESSEQ 3331:3350)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESSEQ 3142:3174)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESSEQ 3175:3225)
13	X-RAY DIFFRACTION	13	(CHAIN C AND RESSEQ 3226:3262)
14	X-RAY DIFFRACTION	14	(CHAIN C AND RESSEQ 3263:3330)
15	X-RAY DIFFRACTION	15	(CHAIN C AND RESSEQ 3331:3359)

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