PDB-6tcb: Crystal structure of protein PA2723 from Pseudomonas aeruginosa PAO1

ID or keywords:

Entry

Database: PDB / ID: 6tcb

Title

Crystal structure of protein PA2723 from Pseudomonas aeruginosa PAO1

Components

Uncharacterized protein PA2723

Keywords

UNKNOWN FUNCTION

Function / homology

metal ion binding / SAM-dependent methyltransferase

Function and homology information

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 1.35 Å

Authors

Popp, M.A. / Blankenfeldt, W.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Crystal structure of protein PA2723 from Pseudomonas aeruginosa PAO1
Authors: Popp, M.A. / Blankenfeldt, W.

History

Deposition	Nov 5, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6tcb.cif.gz	130.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6tcb.ent.gz	102.6 KB	Display	PDB format
PDBx/mmJSON format	6tcb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tc/6tcb ftp://data.pdbj.org/pub/pdb/validation_reports/tc/6tcb	HTTPS FTP

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Related structure data

Similar structure data	3vm8-1 1cde-1 3f2k-2 1cde-4 4zz2-d 3gar-d 1j08-3 1rbz-2 1j08-5 1cde-3 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: Uncharacterized protein PA2723

B: Uncharacterized protein PA2723

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS, light scattering

Unit cell

Length a, b, c (Å)	33.004, 33.028, 41.338
Angle α, β, γ (deg.)	93.920, 103.170, 118.330
Int Tables number	1
Space group name H-M	P1
Symmetry operation	#1: x,y,z

#1: Protein	Uncharacterized protein PA2723 Mass: 10547.978 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA2723 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I0B9
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.79 Å³/Da / Density % sol: 31.34 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Reservoir solution: 1:10 dilution of 0.2% (w/v) caffeine, cytosine, nicotinamide, gallic acid, tetrasodium pyrophosphate and 0.02 M HEPES pH 6.8 in 19% (w/v) PEG3350 and 0.3 M CaCl2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, DESY

/ Beamline: P11 / Wavelength: 1.0332 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 12, 2015

Radiation

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

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection

Resolution: 1.35→39.39 Å / Num. obs: 30273 / % possible obs: 94 % / Redundancy: 3.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.037 / R_pim(I) all: 0.023 / R_rim(I) all: 0.044 / Net I/σ(I): 17.7 / Num. measured all: 105451

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.35-1.37	3.1	0.832	4731	1508	0.731	0.549	1.001	1.7	91.7
7.39-39.39	3.8	0.021	733	193	1	0.012	0.025	48.4	97.5

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Processing

Software

Name	Version	Classification
PDB_EXTRACT		data extraction
PHENIX	1.17rc1_3603	refinement
SHELXE		model building
Coot		model building
Arcimboldo		phasing
Aimless		data scaling
XDS		data reduction

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.35→39.39 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 17.97

	R_factor	Num. reflection	% reflection
R_free	0.1646	1500	4.96 %
R_work	0.1499	-	-
obs	0.1507	30261	94.01 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 92.99 Å² / B_iso mean: 19.9851 Å² / B_iso min: 6.25 Å²

Refinement step

Cycle: final / Resolution: 1.35→39.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1459	0	1	281	1741
B_iso mean	-	-	18.01	32.27	-
Num. residues	-	-	-	-	188

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 11

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.35-1.39	0.2961	120	0.2832	2562	2682	92
1.39-1.44	0.2683	131	0.2494	2572	2703	92
1.44-1.5	0.229	136	0.1948	2582	2718	92
1.5-1.57	0.1875	129	0.1617	2587	2716	93
1.57-1.65	0.1599	151	0.1555	2609	2760	94
1.65-1.76	0.1514	131	0.1498	2609	2740	95
1.76-1.89	0.1813	112	0.1525	2664	2776	94
1.89-2.08	0.1689	147	0.1432	2650	2797	96
2.08-2.38	0.1547	162	0.1338	2639	2801	96
2.38-3	0.1396	132	0.142	2649	2781	95
3-39.39	0.1525	149	0.1339	2638	2787	96

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	0.3867	-0.1522	-0.3647	0.2146	-0.0153	0.3787	-0.0181	0.0507	0.0251	-0.1306	0.0723	0.0648	-0.0452	0.0491	0.0315	0.141	-0.0207	0.0057	0.0975	0.0012	0.0898	-2.0705	14.0151	3.0095
2	0.3136	0.0027	-0.2655	0.0228	0.0429	0.3219	-0.1526	-0.0216	-0.021	-0.1633	0.1172	-0.0114	-0.0841	0.1146	-0.0302	0.1072	-0.0114	-0.0079	0.086	-0.0015	0.0923	1.2262	8.8613	10.4704
3	0.0831	0.0218	-0.0201	0.089	-0.0077	0.096	0.0457	-0.0503	0.0452	0.0023	-0.0575	0.1066	-0.1517	0.0295	-0.001	0.1184	0.0053	-0.0064	0.0854	0.002	0.0978	-4.7045	15.7805	12.2548
4	0.1255	0.059	-0.0666	0.3164	0.187	0.173	-0.0527	0.0368	-0.0359	-0.0362	-0.0515	0.1196	-0.0621	0.0035	-0.05	0.1013	0.0202	-0.0152	0.0961	-0.0025	0.0914	-6.0401	9.5311	13.052
5	0.0963	-0.1259	-0.0684	0.3024	-0.0813	0.2635	0.0423	-0.0794	-0.0734	0.0022	-0.0205	-0.0036	0.0498	-0.0201	0.0208	0.0721	0.0043	-0.0019	0.076	0.0022	0.0872	-0.9794	3.9433	15.4085
6	0.0795	-0.0474	-0.1061	0.1774	0.2195	0.2202	0.041	-0.1215	0.1397	0.0829	0.0304	-0.1016	0.0407	0.0414	0.0363	0.0893	0.0166	-0.002	0.1077	-0.0038	0.1146	4.5928	-3.8988	17.1839
7	0.0835	-0.06	0.0112	0.0466	0.0281	0.0726	-0.0347	0.3896	0.0918	-0.1114	-0.0078	-0.0924	0.0286	0.0189	-0	0.1104	0.0048	-0.0044	0.1229	0.025	0.1508	7.2772	-2.9201	9.144
8	0.1539	-0.0022	-0.0308	0.0853	0.0864	0.2947	0.0102	-0.1937	0.1104	0.0642	0.0123	0.0322	0.0443	0.0383	0.0054	0.1376	-0.0128	0.003	0.1468	-0.0132	0.114	2.349	9.9414	37.856
9	0.1154	0.178	0.0708	0.2326	0.2115	0.3996	0.1574	-0.1542	0.1803	0.1337	-0.2333	0.249	-0.2686	0.0271	0.0013	0.1568	-0.0142	-0.0038	0.1301	-0.0093	0.119	-4.6821	10.9167	30.6182
10	0.1044	0.1283	0.1257	0.1257	0.1138	0.0884	0.0658	0.096	-0.1213	-0.0398	0.0178	-0.044	-0.2276	0.2665	-0	0.1182	-0.0064	0.0026	0.1243	0.0035	0.109	4.3554	9.6398	28.4394
11	0.0976	0.0398	-0.0547	0.1496	0.0629	0.1069	-0.0498	-0.1603	-0.0854	0.1581	0.0899	-0.3103	-0.0131	-0.1097	0.014	0.1212	0.0265	-0.0324	0.103	0.0143	0.1334	1.7405	4.3294	28.2959
12	0.021	-0.0027	-0.0093	0.0076	-0.0275	0.0358	-0.0934	0.0498	0.4015	0.0302	-0.038	0.1614	-0.3015	-0.314	-0.003	0.1475	0.0479	0.0125	0.1486	-0.0107	0.2188	-9.1392	13.6593	23.3442
13	0.0843	0.0263	-0.1134	0.0591	0.0063	0.1631	0.0135	0.0439	-0.0157	0.079	-0.0222	0.0298	0.1063	-0.0315	-0	0.1084	-0.0039	0.0125	0.1092	0.0094	0.0869	-4.3037	0.6351	27.2704
14	0.1646	0.0937	-0.1815	0.0947	-0.0403	0.1482	-0.0472	0.3362	0.0734	-0.0983	0.0738	0.063	-0.022	-0.1049	0.0228	0.1035	0.0117	-0.0088	0.1946	0.0107	0.1464	-15.7415	8.2109	23.1462
15	0.0929	0.0802	-0.0387	0.0691	-0.0213	0.0438	-0.1099	-0.0341	-0.0603	0.0396	0.2941	0.4191	0.0784	0.0568	0	0.146	0.0098	-0.0053	0.175	0.0497	0.2137	-17.5852	10.5284	31.7392

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 18 )	A	-1 - 18
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 30 )	A	19 - 30
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 41 )	A	31 - 41
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 42 through 51 )	A	42 - 51
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 52 through 64 )	A	52 - 64
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 65 through 80 )	A	65 - 80
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 81 through 92 )	A	81 - 92
8	X-RAY DIFFRACTION	8	chain 'B' and (resid -1 through 18 )	B	-1 - 18
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 19 through 30 )	B	19 - 30
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 31 through 41 )	B	31 - 41
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 42 through 49 )	B	42 - 49
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 50 through 56 )	B	50 - 56
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 57 through 64 )	B	57 - 64
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 65 through 80 )	B	65 - 80
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 81 through 92 )	B	81 - 92

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