PDB-8aid: Crystal structure of N-terminally truncated PA4183 from P. aerugi...

ID or keywords:

Entry

Database: PDB / ID: 8aid

Title

Crystal structure of N-terminally truncated PA4183 from P. aeruginosa PAO1

Components

PA4183

Keywords

UNKNOWN FUNCTION / PA4183 / P. aeruginosa

Function / homology

2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta / VOC family protein

Function and homology information

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.52 Å

Authors

Popp, M.A. / Blankenfeldt, W.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Structure of N-terminally truncated PA4183 from P. aeruginosa PAO1
Authors: Popp, M.A. / Blankenfeldt, W. / Vit, A.

History

Deposition	Jul 26, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 30, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8aid.cif.gz	347.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8aid.ent.gz	290.9 KB	Display	PDB format
PDBx/mmJSON format	8aid.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8aid_validation.pdf.gz	454.8 KB	Display	wwPDB validaton report
Full document	8aid_full_validation.pdf.gz	455.9 KB	Display
Data in XML	8aid_validation.xml.gz	30.9 KB	Display
Data in CIF	8aid_validation.cif.gz	46.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ai/8aid ftp://data.pdbj.org/pub/pdb/validation_reports/ai/8aid	HTTPS FTP

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PA4183

B: PA4183

C: PA4183

D: PA4183

hetero molecules

63.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PA4183

B: PA4183

hetero molecules

defined by author&software
Evidence: gel filtration
31.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: PA4183

D: PA4183

hetero molecules

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

Unit cell

Length a, b, c (Å)	155.492, 155.492, 59.516
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-480- HOH
2	1	B-381- HOH
3	1	B-452- HOH
4	1	C-371- HOH
5	1	D-446- HOH

#1: Protein	PA4183 Mass: 15595.638 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA4183 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HWJ8
#2: Chemical	ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES Mass: 207.290 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₈H₁₇NO₃S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 774 / 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: 3.3 Å³/Da / Density % sol: 63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.6 Details: 0.7 M K/NA tartrate, 0.2 M LiSO4, 0.1 M CHES pH 9.6

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.2 / Wavelength: 0.91841 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 5, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.91841 Å / Relative weight: 1

Reflection

Resolution: 1.52→47.26 Å / Num. obs: 126391 / % possible obs: 99.8 % / Redundancy: 5.4 % / B_iso Wilson estimate: 19.35 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.045 / R_pim(I) all: 0.021 / R_rim(I) all: 0.049 / Net I/σ(I): 19.1 / Num. measured all: 682412

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
1.52-1.55	3.5	0.619	20968	6076	0.795	0.369	0.725	2	98
8.33-47.26	4.7	0.032	3717	789	0.998	0.016	0.036	42.5	94.4

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4459	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.52→22.3 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1658	6504	5.15 %
R_work	0.1487	119726	-
obs	0.1496	126230	99.75 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 147.21 Å² / B_iso mean: 30.041 Å² / B_iso min: 12.61 Å²

Refinement step

Cycle: final / Resolution: 1.52→22.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4262	0	116	774	5152
B_iso mean	-	-	35.56	38	-
Num. residues	-	-	-	-	550

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.52-1.54	0.2619	206	0.2545	3866	4072	97
1.54-1.56	0.2618	181	0.2316	3977	4158	99
1.56-1.57	0.2422	219	0.2176	3952	4171	100
1.57-1.59	0.2061	246	0.1974	3943	4189	100
1.59-1.62	0.1929	221	0.1885	3992	4213	100
1.62-1.64	0.1898	216	0.181	3935	4151	100
1.64-1.66	0.1704	222	0.1718	4002	4224	100
1.66-1.69	0.2016	213	0.1755	3971	4184	100
1.69-1.71	0.2216	186	0.1897	4019	4205	100
1.71-1.74	0.1814	221	0.1797	3958	4179	100
1.74-1.77	0.2014	195	0.1799	4008	4203	100
1.77-1.8	0.1879	217	0.1674	3980	4197	100
1.8-1.84	0.1973	237	0.1563	3943	4180	100
1.84-1.87	0.164	218	0.1516	4002	4220	100
1.87-1.91	0.1807	217	0.1458	3984	4201	100
1.91-1.96	0.1578	214	0.1508	4009	4223	100
1.96-2.01	0.1683	215	0.1519	3974	4189	100
2.01-2.06	0.183	209	0.1501	3988	4197	100
2.06-2.12	0.161	238	0.146	3987	4225	100
2.12-2.19	0.154	194	0.1412	4033	4227	100
2.19-2.27	0.1561	220	0.1402	3964	4184	100
2.27-2.36	0.1403	206	0.145	4040	4246	100
2.36-2.47	0.1668	202	0.1413	4021	4223	100
2.47-2.6	0.1722	232	0.1503	4000	4232	100
2.6-2.76	0.1784	204	0.155	4024	4228	100
2.76-2.97	0.1695	241	0.1545	4017	4258	100
2.97-3.27	0.1607	233	0.1527	4011	4244	100
3.27-3.74	0.1575	233	0.1288	4025	4258	100
3.74-4.71	0.136	192	0.1154	4078	4270	100
4.71-22.3	0.1578	256	0.1527	4023	4279	97

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	0.0156	0.0789	0.0405	-0.062	0.0243	0.028	-0.0243	0.2419	-0.07	-0.0989	-0.045	0.1584	0.0481	-0.0329	-0.0275	0.3177	-0.0596	-0.0621	0.3856	-0.0518	0.1772	-67.6065	207.8379	-17.4935
2	0.242	0.3634	-0.1543	0.8603	0.1548	0.6242	-0.0865	0.0503	-0.0524	-0.0554	0.0342	0.0732	-0.0388	-0.0024	-0	0.1536	-0.0028	-0.0128	0.198	-0.0082	0.1489	-60.0756	207.9319	-1.8319
3	0.0403	-0.03	0.0636	0.1351	-0.1696	0.125	0.039	-0.0061	0.058	-0.1124	-0.0699	0.1581	0.0545	-0.1415	0.0227	0.227	-0.0196	-0.0527	0.2724	-0.028	0.1625	-64.7925	209.2048	-8.7326
4	1.0197	0.1441	0.0327	0.6671	-0.1911	0.4796	-0.1164	0.1701	-0.2217	-0.1024	0.0432	0.1433	0.017	-0.0461	-0.1416	0.138	-0.0293	0.01	0.1981	-0.0595	0.215	-65.2823	196.1601	-3.7395
5	0.2109	-0.0555	0.1221	0.014	-0.0191	0.0625	0.0455	0.4821	-0.143	-0.0912	-0.2414	0.3763	0.0684	-0.1879	-0.0253	0.2837	-0.0577	-0.0187	0.3238	-0.1592	0.2258	-62.7676	195.7835	-14.6139
6	0.5314	-0.0376	0.0048	0.3748	0.2814	0.1103	-0.0536	0.1767	-0.334	-0.1347	-0.0546	0.1526	-0.0667	-0.0352	-0.0259	0.2039	-0.0145	0.0149	0.2348	-0.069	0.1809	-60.5598	195.5081	-6.9853
7	0.2742	-0.0489	-0.0547	0.333	0.1783	0.0984	-0.098	-0.0332	-0.0924	0.059	0.1257	-0.4131	-0.081	0.1203	0.0166	0.1714	0.0175	-0.056	0.2366	0.0226	0.3092	-45.997	201.455	16.043
8	0.3175	-0.0767	0.0364	0.1776	-0.0281	0.069	-0.1475	-0.0478	-0.269	0.0643	0.0329	-0.0176	0.0639	0.0248	-0.182	0.1803	0.0217	0.0715	0.1836	0.0201	0.2838	-57.0889	189.395	10.9179
9	0.4343	0.3155	0.042	0.3319	-0.086	0.0163	-0.073	-0.1309	-0.147	0.1022	0.0344	-0.1416	-0.0267	0.0024	-0	0.1905	0.0388	0.0148	0.2216	0.0372	0.2235	-54.46	193.2711	17.5471
10	0.5711	-0.136	-0.229	0.3849	-0.2117	-0.2083	-0.0706	-0.1651	-0.0423	0.2048	0.071	0.0916	-0.0424	0.0724	-0.0005	0.2011	0.0165	0.0293	0.2107	0.0112	0.1653	-62.274	205.9629	16.7156
11	0.0884	0.1099	-0.014	0.2159	0.0571	0.0352	-0.1347	-0.224	0.0884	0.0337	-0.2471	0.3778	0.3204	-0.0542	-0.0175	0.2483	-0.0131	0.0861	0.2533	0.0019	0.2864	-68.9768	211.3017	18.2788
12	0.8325	0.9132	-0.0333	1.0136	-0.0289	-0.0079	-0.079	-0.5788	-0.5246	0.5201	-0.0878	-0.5091	-0.3148	-0.1552	-0.0087	0.4492	0.1337	-0.0633	0.4456	0.0311	0.1266	-56.1302	205.6288	25.2662
13	0.3102	0.2343	-0.2483	0.6947	0.2334	0.2029	-0.0041	-0.0964	-0.0679	0.3102	-0.0047	0.0025	0.044	-0.0132	0.0004	0.2157	0.0123	-0.0208	0.2125	0.0179	0.165	-58.1466	206.5723	17.4422
14	0.3133	0.109	0.1091	0.2774	0.328	0.1989	-0.0486	0.1491	-0.1634	-0.0698	-0.0271	-0.0859	0.161	0.0577	0	0.2583	0.0073	0.0157	0.2473	-0.0177	0.1612	-42.3578	224.1269	-10.9298
15	0.2298	-0.0844	0.0832	0.0672	0.0581	0.2031	-0.0052	0.0847	0.2476	0.0091	-0.0195	-0.0247	0.0216	-0.0535	-0.0141	0.1608	0.0238	0.0049	0.1591	0.0431	0.2265	-39.271	238.3915	-3.3846
16	0.0336	0.0274	0.048	0.0259	0.0056	0.012	-0.0074	0.0014	0.2289	-0.0784	-0.0079	-0.2688	0.015	-0.029	0	0.1875	0.0238	0.0324	0.198	0.0434	0.3132	-29.0919	236.0499	-4.6113
17	0.0803	0.2288	0.1016	0.4023	0.2044	0.0503	-0.3098	0.0956	0.3217	-0.0959	0.0903	-0.1504	-0.2076	-0.0771	-0.0001	0.2842	0.0277	-0.0292	0.256	0.0361	0.2333	-39.3042	234.0272	-12.2919
18	0.3197	0.3833	-0.0192	0.302	0.0482	-0.005	0.0038	0.1508	0.3083	-0.112	-0.003	0.1037	0.0106	0.0558	-0	0.1951	0.0228	-0.0096	0.1831	0.0705	0.2807	-42.9357	241.4663	-5.8863
19	0.0845	-0.0784	-0.0259	0.0541	0.0176	0.0384	0.0287	-0.0241	0.0131	0.026	-0.0511	0.1127	0.0692	-0.0364	0.0001	0.1863	0.0105	-0.012	0.1891	-0.0025	0.1874	-49.2953	226.0747	-2.2953
20	0.0547	0.0715	-0.074	0.0432	-0.013	0.046	-0.0152	0.009	0.192	-0.1073	0.0736	0.2766	0.0688	0.0211	-0	0.1664	0.0179	-0.0226	0.1729	0.0135	0.2023	-60.1847	226.8374	1.2128
21	0.0972	0.1796	0.0377	0.3061	0.1624	0.032	0.1362	0.1365	0.1873	-0.2775	-0.132	0.105	-0.364	-0.0965	0	0.2442	0.0511	-0.0272	0.2278	0.027	0.2219	-56.4377	234.7595	-5.9647
22	0.2686	0.2703	0.1173	0.2025	0.1552	-0.0001	0.0006	0.0564	0.2588	-0.0275	0.0458	0.0892	0.0238	-0.0349	0	0.1958	0.0198	-0.0065	0.1869	0.0149	0.1879	-52.6279	233.1719	-0.111
23	0.2346	0.1669	0.0382	0.132	0.0248	0.0131	0.21	0.4077	0.0877	-0.5041	-0.0302	0.1918	0.0156	0.2726	0.2208	0.4273	0.0114	0.0163	0.4648	-0.0289	0.0721	-47.3159	223.6885	-18.1877
24	0.2616	0.1779	-0.1255	0.2964	-0.0991	0.1488	-0.0643	0.0306	-0.24	0.0972	-0.0401	-0.3733	0.1084	-0.1884	-0.0445	0.2011	-0.0019	-0.0603	0.2438	0.0028	0.1728	-36.1903	220.4757	15.1152
25	0.1839	0.2089	-0.0679	0.3168	-0.2647	0.2453	0.055	-0.1308	0.207	0.0563	-0.0406	0.0539	0.0213	-0.0136	-0.0001	0.1822	0	0.0084	0.2095	-0.0486	0.1658	-50.2878	230.4722	13.9539
26	0.1838	-0.2818	-0.0001	0.343	-0.0492	0.0234	-0.129	-0.3597	0.0175	0.0633	0.0182	0.0283	-0.3507	-0.1216	-0.0066	0.2909	-0.0036	-0.0505	0.2897	-0.0565	0.1108	-43.5764	227.7554	21.0837
27	0.483	0.1718	-0.1188	0.7174	-0.1181	0.413	0.1008	-0.2015	0.2562	0.1616	-0.0404	-0.1435	-0.0247	0.0235	0.0037	0.1926	-0.0092	-0.0175	0.2018	-0.0747	0.222	-36.8723	235.2687	13.9844
28	0.3871	0.0069	-0.098	0.3826	0.0444	0.0307	0.0895	-0.2621	0.3463	0.1947	-0.0397	-0.1931	-0.1071	0.0246	0.009	0.2228	-0.0205	-0.0358	0.2254	-0.0503	0.2802	-31.28	237.2896	12.6355
29	0.2556	-0.2816	-0.0982	0.3131	0.1048	0.0338	0.3336	-0.3472	-0.0535	0.4925	0.089	-0.3181	0.2049	0.1466	0.1321	0.3932	-0.0385	-0.1415	0.438	0.0699	0.1328	-32.0427	220.8379	24.5296

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 8 )	A	-1 - 8
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 9 through 43 )	A	9 - 43
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 44 through 56 )	A	44 - 56
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 57 through 107 )	A	57 - 107
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 108 through 114 )	A	108 - 114
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 115 through 139 )	A	115 - 139
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 4 through 19 )	B	4 - 19
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 20 through 43 )	B	20 - 43
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 44 through 70 )	B	44 - 70
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 71 through 100 )	B	71 - 100
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 101 through 107 )	B	101 - 107
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 108 through 114 )	B	108 - 114
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 115 through 139 )	B	115 - 139
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 3 through 19 )	C	3 - 19
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 20 through 31 )	C	20 - 31
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 32 through 43 )	C	32 - 43
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 44 through 56 )	C	44 - 56
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 57 through 83 )	C	57 - 83
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 84 through 90 )	C	84 - 90
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 91 through 101 )	C	91 - 101
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 102 through 114 )	C	102 - 114
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 115 through 133 )	C	115 - 133
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 134 through 139 )	C	134 - 139
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 4 through 19 )	D	4 - 19
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 20 through 43 )	D	20 - 43
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 44 through 56 )	D	44 - 56
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 57 through 101 )	D	57 - 101
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 102 through 133 )	D	102 - 133
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 134 through 139 )	D	134 - 139

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Feb 9, 2022. New format data for meta-information of EMDB entries

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