PDB-2igs: Crystal Structure of the Protein of Unknown Function from Pseudom...

ID or keywords:

Entry

Database: PDB / ID: 2igs

Title

Crystal Structure of the Protein of Unknown Function from Pseudomonas aeruginosa

Components

Hypothetical protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / helix-bundles / alpha-beta / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

PA2222-like fold / PA2222-like domain / Protein of unknown function DUF3218 / PA2222-like domain superfamily / Protein of unknown function (DUF3218) / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.17 Å

Authors

Kim, Y. / Joachimiak, A. / Skarina, T. / Egorova, O. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal Structure of the Hypothetical Protein from Pseudomonas aeruginosa
Authors: Kim, Y. / Joachimiak, A. / Skarina, T. / Egorova, O. / Edwards, A. / Savchenko, A.

History

Deposition	Sep 25, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 24, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.name

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S) ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2igs.cif.gz	368.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2igs.ent.gz	315.6 KB	Display	PDB format
PDBx/mmJSON format	2igs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2igs_validation.pdf.gz	535.5 KB	Display	wwPDB validaton report
Full document	2igs_full_validation.pdf.gz	573.9 KB	Display
Data in XML	2igs_validation.xml.gz	75 KB	Display
Data in CIF	2igs_validation.cif.gz	106.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ig/2igs ftp://data.pdbj.org/pub/pdb/validation_reports/ig/2igs	HTTPS FTP

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Related structure data

Similar structure data	5x9z-1 5gug-1 3wf3-d 3k72-2 5ekq-d 3k6s-3 5es4-4 3m17-d 3wf0-d 4ze8-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC5561

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Hypothetical protein

B: Hypothetical protein

C: Hypothetical protein

D: Hypothetical protein

E: Hypothetical protein

F: Hypothetical protein

G: Hypothetical protein

H: Hypothetical protein

hetero molecules

194 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	76.424, 100.458, 140.845
Angle α, β, γ (deg.)	90.00, 100.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Hypothetical protein Mass: 23985.559 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q9I1P7
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1059 / 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: 2.77 Å³/Da / Density % sol: 55.6 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 25% PEG5K MME, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2004 / Details: mirrors
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97932 Å / Relative weight: 1
Reflection	Resolution: 2.17→28.52 Å / Num. all: 107066 / Num. obs: 107066 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / R_merge(I) obs: 0.104 / Net I/σ(I): 7
Reflection shell	Resolution: 2.17→2.25 Å / Redundancy: 5 % / R_merge(I) obs: 0.597 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9259 / % possible all: 84

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
HKL-3000		phasing
SHELXCD		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
SOLVE		phasing
RESOLVE		phasing
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.17→28.52 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.92 / SU B: 11.73 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.225
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25017	10728	10 %	RANDOM
R_work	0.18728	-	-	-
all	0.19359	96251	-	-
obs	0.19359	96251	96.62 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 21.468 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.5 Å²	0 Å²	-1.04 Å²
2-	-	1.36 Å²	0 Å²
3-	-	-	-2.24 Å²

Refinement step

Cycle: LAST / Resolution: 2.17→28.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13123	0	103	1059	14285

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	14374
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.429	1.97	19647
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.546	5	1866
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.744	24.066	664
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.455	15	2320
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.459	15	109
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	2141
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11313
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	7268
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	10064
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	955
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.219	0.2	164
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.217	0.2	53
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.578	1.5	9271
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.937	2	14600
X-RAY DIFFRACTION	r_scbond_it	1.656	3	5771
X-RAY DIFFRACTION	r_scangle_it	2.47	4.5	5047
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.17→2.226 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.31	649	-
R_work	0.232	5914	-
obs	-	5914	81.2 %

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	2.614	0.4663	0.671	4.7514	0.5986	4.2389	-0.2055	-0.1569	0.1368	-0.3054	0.3404	0.256	-0.1728	-1.1807	-0.1348	-0.0114	0.0759	-0.0124	0.5718	0.0611	0.033	24.87	59.446	-4.473
2	1.3591	-0.0036	0.4147	1.721	-0.8211	4.2678	-0.0868	-0.2063	-0.0368	-0.0266	0.2501	0.0496	0.2213	-0.7502	-0.1633	-0.0158	-0.0208	0.0176	0.4189	0.0107	0.0056	30.235	52.14	-0.204
3	1.7522	0.0993	0.9307	1.1287	-0.1633	3.0762	-0.0578	-0.1928	-0.1678	0.078	0.0856	-0.0295	0.077	-0.3431	-0.0278	0.0464	0.0697	0.011	0.2824	-0.0343	0.0542	40.815	52.611	10.554
4	1.9909	0.2355	-0.8651	2.3235	-0.5909	2.9736	0.003	0.0494	-0.195	0.2115	-0.0238	0.1782	0.0711	-0.1367	0.0208	0.1507	-0.068	-0.0151	0.1132	0.0327	0.1539	-24.531	49.816	46.369
5	0.856	-0.4403	-0.3029	2.2602	-1.3347	3.1883	0.0215	-0.2276	0.0988	0.7512	-0.0973	-0.2537	-0.5696	0.3451	0.0757	0.2237	-0.1548	-0.0465	0.09	0.0163	0.09	-15.83	59.137	55.422
6	4.5177	0.753	0.6915	1.3806	-0.8902	2.865	0.3211	0.3409	0.2494	-0.1644	-0.2098	0.1861	-0.3462	-0.4441	-0.1113	0.0854	-0.006	-0.0109	0.1036	0.0482	0.0049	-27.226	62.59	33.698
7	1.2511	-0.25	-1.1409	0.8082	-0.3182	1.7739	0.1322	0.0952	0.1495	-0.0633	0.0309	0.0246	-0.2431	0.0682	-0.1631	0.0839	-0.0867	-0.0161	0.1372	0.0167	0.0654	-11.745	65.61	32.991
8	3.1341	0.9487	-0.8761	1.6328	-0.14	0.8621	0.1469	-0.0169	-0.1097	0.1328	-0.1204	-0.0987	-0.1714	0.1177	-0.0265	0.1021	-0.0872	-0.0449	0.1442	0.0314	0.0696	-9.59	64.066	38.819
9	1.6886	0.3857	-0.362	3.1573	1.8208	4.9616	-0.0765	0.3423	0.0622	-0.1851	0.0526	0.3169	0.0342	-0.6406	0.0239	0.0813	-0.2114	-0.08	0.3973	0.096	0.13	-5.898	88.656	22.179
10	1.5351	0.2922	-0.8003	2.4145	1.4713	4.8241	0.0741	0.1813	0.2017	-0.1208	-0.0888	0.2117	-0.2826	-0.4005	0.0146	0.0911	-0.1105	-0.0505	0.2481	0.116	0.1153	2.064	95.924	23.301
11	1.3543	0.2563	-0.3961	1.0074	0.4513	1.8652	0.0372	-0.041	0.0245	0.1484	-0.0901	0.1116	0.226	-0.1877	0.0529	0.2081	-0.1353	-0.0051	0.1556	0.0532	0.1071	3.746	87.298	39.7
12	1.7375	1.1843	1.0711	0.9116	0.1996	3.3566	0.1858	0.1442	-0.215	0.1149	0.0533	-0.1755	0.5542	0.1885	-0.2391	0.1328	-0.0788	-0.0366	0.0937	0.0107	0.0641	15.08	83.965	37.416
13	4.3363	1.76	-0.6441	2.8566	1.3105	1.5275	0.0269	0.3086	-0.0524	0.2215	-0.0107	-0.1256	0.2615	-0.0031	-0.0162	0.1569	-0.1307	-0.019	0.1961	0.0269	0.06	7.808	88.507	33.982
14	2.066	-1.0014	0.9652	4.4605	-0.9672	3.7076	-0.1865	-0.043	-0.0532	0.3031	0.2631	-0.3962	0.0514	0.7651	-0.0766	-0.027	0.0033	-0.0351	0.3951	-0.0656	0.1018	27.914	54.372	44.799
15	1.2409	-0.2498	0.238	1.9218	0.5187	3.04	-0.1316	0.1062	0.0387	0.0277	0.1571	-0.1684	-0.0056	0.4664	-0.0255	0.0171	-0.0164	-0.01	0.2647	-0.0323	0.0619	20.81	54.224	41.079
16	1.4973	-0.494	0.4311	1.0832	0.3852	2.1789	-0.109	0.1716	-0.1261	-0.1053	0.1242	0.0603	0.1365	0.1926	-0.0152	0.0617	-0.0727	0.0157	0.2066	0.0077	0.0591	9.795	51.913	29.779
17	1.1976	-0.5139	2.1726	11.1238	-0.4798	4.4905	-0.169	0.2078	0.0945	-1.1758	0.0693	0.0141	-0.3765	0.5686	0.0997	0.2082	0.0044	0.0212	0.1281	-0.0002	-0.0457	17.994	60.11	60.354
18	1.0485	0.9464	0.7499	2.5919	1.1209	2.9775	-0.1259	0.0907	0.0473	-0.3401	0.0126	0.2152	-0.0733	0.0894	0.1133	0.109	0.0405	-0.0115	0.0914	0.0055	0.0558	11.47	55.27	65.908
19	1.3511	1.3289	-0.0136	2.674	-1.0864	2.4291	0.2628	-0.1251	0.0709	0.305	-0.1216	0.003	-0.058	0.0055	-0.1412	0.0931	0.0121	-0.0354	0.0651	-0.007	0.1198	7.226	55.744	84.164
20	0.6259	1.4567	-0.6941	3.4744	-1.1346	3.5312	-0.0751	0.034	0.3179	-0.2011	0.2449	0.8686	0.0484	-0.4693	-0.1698	0.1103	0.1049	-0.0993	0.1376	0.0414	0.2886	-4.248	58.239	76.66
21	2.1143	0.5164	-0.5723	7.1332	-1.4563	0.4023	-0.1201	-0.0423	0.0175	-0.1179	0.0139	-0.0642	-0.0273	0.0623	0.1062	0.1403	0.0529	-0.0381	0.0825	0.0068	0.1199	8.871	59.61	75.977
22	1.7286	0.3624	0.176	2.1938	0.4297	3.5471	0.0491	0.2525	-0.085	-0.1689	-0.0332	-0.0845	0.1939	0.3933	-0.0159	0.0493	0.0971	-0.0121	0.2458	-0.0817	0.0281	-3.191	50.602	-6.428
23	2.943	-0.1997	2.1376	1.0901	-0.4632	5.8937	0.0372	0.3608	0.2031	-0.1068	-0.0196	-0.0051	-0.4027	0.3724	-0.0176	0.0597	-0.014	-0.0027	0.1247	0.0243	-0.0135	-3.397	63.96	-5.419
24	2.0794	0.7843	-0.7774	1.0132	0.4596	4.3536	0.0221	0.1673	0.303	-0.0569	0.077	-0.0102	-0.7492	-0.2695	-0.0992	0.08	0.0423	-0.0399	0.0839	-0.0103	0.0187	-13.684	66.304	6.633
25	3.4223	-0.2903	-0.1872	0.9471	-0.3896	3.3732	-0.0635	0.0419	0.1173	-0.1049	0.0367	0.137	-0.4131	-0.1743	0.0267	0.0897	0.0443	-0.0416	0.0919	-0.0052	0.0155	-16.126	65.073	3.76
26	2.0962	-0.3701	0.2366	3.8272	-1.12	3.8087	0.2237	0.278	0.058	-0.1742	-0.1926	-0.2053	0.0871	0.4203	-0.0311	0.0247	0.0171	0.0428	0.2678	0.029	0.0215	43.396	104.89	25.818
27	1.523	0.2125	0.1729	1.5266	0.2939	3.0491	0.1049	0.2549	0.1686	-0.0134	-0.0655	-0.0762	-0.3384	-0.0399	-0.0394	0.0734	-0.0021	0.0437	0.1639	0.0727	0.0714	35.599	112.596	28.433
28	1.5932	-0.2947	-0.0616	1.9026	-0.5907	3.2683	0.1563	-0.0093	0.1553	0.1391	-0.0505	-0.0173	-0.2429	-0.2962	-0.1058	0.0573	-0.0408	0.0124	0.1235	0.0172	0.0437	27.407	108.08	42.725
29	2.7074	0.3399	0.3289	1.4355	0.0363	1.8589	0.1878	0.0097	0.2031	0.0595	-0.099	0.1041	-0.1492	-0.2381	-0.0888	0.0845	0.006	0.0124	0.1019	0.038	0.0445	24.807	108.296	38.342
30	0.4974	-0.3217	-1.1682	4.476	-1.814	5.0721	-0.0109	-0.0691	0.0602	0.3851	0.0672	-0.3157	-0.0088	0.4643	-0.0562	0.0463	0.0434	-0.0703	0.0993	-0.0534	0.1116	6.569	87.715	75.826
31	0.5831	-0.3696	0.0518	2.5019	0.7544	3.0187	0.0071	-0.028	0.1047	0.0493	0.0432	-0.1429	0.0537	0.1401	-0.0503	0.068	0.019	-0.0013	0.0546	-0.0249	0.1105	0.269	89.6	70.929
32	6.0699	-0.323	1.2589	4.1626	0.1931	1.8038	0.2226	0.6342	0.0836	-1.1895	-0.2629	0.5217	-0.4669	0.0473	0.0403	0.3302	0.1251	-0.1003	0.0801	-0.0412	0.0794	-7.8	93.254	53.361
33	0.0866	-0.4539	0.1953	5.4068	1.1983	2.0727	0.1006	0.0544	-0.1019	-0.3961	-0.1937	0.9016	0.2342	-0.3584	0.0931	0.0717	0.0347	-0.0878	0.0922	-0.0527	0.2191	-13.879	83.115	59.823
34	3.959	-0.3814	-0.084	5.9638	0.025	1.9106	0.1946	0.2121	0.0937	-0.163	-0.1796	0.5101	-0.0567	-0.2343	-0.015	0.0874	0.0428	-0.0147	0.0856	-0.0201	0.1057	-9.802	87.914	63.249

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	4 - 61	6 - 63
2	X-RAY DIFFRACTION	2	A	A	62 - 124	64 - 126
3	X-RAY DIFFRACTION	3	A	A	125 - 217	127 - 219
4	X-RAY DIFFRACTION	4	B	B	2 - 64	4 - 66
5	X-RAY DIFFRACTION	5	B	B	65 - 102	67 - 104
6	X-RAY DIFFRACTION	6	B	B	103 - 124	105 - 126
7	X-RAY DIFFRACTION	7	B	B	125 - 169	127 - 171
8	X-RAY DIFFRACTION	8	B	B	170 - 215	172 - 217
9	X-RAY DIFFRACTION	9	C	C	4 - 44	6 - 46
10	X-RAY DIFFRACTION	10	C	C	45 - 91	47 - 93
11	X-RAY DIFFRACTION	11	C	C	92 - 148	94 - 150
12	X-RAY DIFFRACTION	12	C	C	149 - 191	151 - 193
13	X-RAY DIFFRACTION	13	C	C	192 - 216	194 - 218
14	X-RAY DIFFRACTION	14	D	D	4 - 48	6 - 50
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19	X-RAY DIFFRACTION	19	E	E	107 - 162	109 - 164
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21	X-RAY DIFFRACTION	21	E	E	200 - 216	202 - 218
22	X-RAY DIFFRACTION	22	F	F	2 - 76	4 - 78
23	X-RAY DIFFRACTION	23	F	F	77 - 123	79 - 125
24	X-RAY DIFFRACTION	24	F	F	124 - 175	126 - 177
25	X-RAY DIFFRACTION	25	F	F	176 - 216	178 - 218
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27	X-RAY DIFFRACTION	27	G	G	63 - 123	65 - 125
28	X-RAY DIFFRACTION	28	G	G	124 - 171	126 - 173
29	X-RAY DIFFRACTION	29	G	G	172 - 217	174 - 219
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31	X-RAY DIFFRACTION	31	H	H	45 - 117	47 - 119
32	X-RAY DIFFRACTION	32	H	H	118 - 141	120 - 143
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34	X-RAY DIFFRACTION	34	H	H	187 - 217	189 - 219

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