PDB-2xu8: Structure of Pa1645

ID or keywords:

Entry

Database: PDB / ID: 2xu8

Title

Structure of Pa1645

Components

PA1645

Keywords

STRUCTURAL GENOMICS / BACTERIAL VIRULENCE

Function / homology

Domain of unknown function (DUF5086) / Protein of unknown function DUF5086 / Domain of unknown function DUF5086 superfamily / Domain of unknown function (DUF5086) / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta / DUF5086 domain-containing protein

Function and homology information

Biological species

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.98 Å

Authors

Abdelli, W.B. / Moynie, L. / McMahon, S.A. / Liu, H. / Alphey, M.S. / Naismith, J.H.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The Aeropath Project Targeting Pseudomonas Aeruginosa: Crystallographic Studies for Assessment of Potential Targets in Early-Stage Drug Discovery
Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M.S. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / ...

History

Deposition	Oct 15, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 29, 2010	Provider: repository / Type: Initial release
Revision 1.1	Mar 14, 2012	Group: Structure summary
Revision 1.2	Jan 9, 2013	Group: Database references / Version format compliance
Revision 1.3	Jan 23, 2013	Group: Database references
Revision 1.4	Aug 19, 2015	Group: Source and taxonomy / Structure summary
Revision 1.5	Oct 9, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2xu8.cif.gz	161.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2xu8.ent.gz	132 KB	Display	PDB format
PDBx/mmJSON format	2xu8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xu/2xu8 ftp://data.pdbj.org/pub/pdb/validation_reports/xu/2xu8	HTTPS FTP

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Related structure data

Related structure data	4avfC 4avrC 4avyC 4b79C 4b7cC 4b7xC 4b9aC 4b9eC 4es6C 4etrC 4exaC 4exbC C: citing same article (ref.)
Similar structure data	7ao7-5 4yzr-d 6rqd-d 3nc7-2 3nc6-1 4fmx-2 1rom-d 7abb-d 2y5z-2 6t0g-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PA1645

B: PA1645

C: PA1645

hetero molecules

40.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	125.970, 125.970, 125.840
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

#1: Protein	PA1645 Mass: 13117.771 Da / Num. of mol.: 3 / Fragment: RESIDUES 20-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I380
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	FIRST 19 RESIDUES REMOVED FROM CONSTRUCT

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density % sol: 60 % / Description: NONE
Crystal grow	pH: 4.5 / Details: pH 4.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.6
Detector	Type: ADSC CCD / Detector: CCD / Date: Jul 2, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.6 Å / Relative weight: 1
Reflection	Resolution: 1.98→89 Å / Num. obs: 35545 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 73 % / R_merge(I) obs: 0.09 / Net I/σ(I): 56.5
Reflection shell	Resolution: 1.98→2.03 Å / Redundancy: 74 % / R_merge(I) obs: 0.75 / Mean I/σ(I) obs: 9 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0081	refinement
xia2		data reduction
xia2		data scaling

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.98→89.07 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.949 / SU B: 4.903 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19226	1778	5 %	RANDOM
R_work	0.17622	-	-	-
obs	0.17705	33751	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 35.255 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.48 Å²	0 Å²	0 Å²
2-	-	0.48 Å²	0 Å²
3-	-	-	-0.96 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→89.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2784	0	55	246	3085

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.021	2991
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	2053
X-RAY DIFFRACTION	r_angle_refined_deg	1.206	1.958	4109
X-RAY DIFFRACTION	r_angle_other_deg	1.017	3	4942
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.568	5	369
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.534	22.583	151
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.48	15	453
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.63	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	417
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	3372
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	644
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.978→2.029 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.211	135	-
R_work	0.181	2465	-
obs	-	-	100 %

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	5.7009	0.0488	0.7794	4.1095	-1.7875	2.6947	-0.3386	0.4908	-0.1914	-0.5546	0.2262	-0.0324	0.1157	-0.0462	0.1124	0.186	-0.0898	0.0471	0.1233	-0.024	0.0614	82.079	29.644	-21.392
2	87.0825	39.9438	-14.4608	40.2836	-6.1552	9.0547	0.2759	-1.9452	-2.9669	0.2457	-1.4438	-3.542	0.869	0.5677	1.1678	0.1889	0.0757	0.0615	0.21	0.1711	0.4727	85.912	15.932	-7.548
3	1.4561	0.8744	0.5569	6.4094	-4.608	4.4365	-0.2502	0.0116	-0.0003	-0.2579	0.1413	-0.1062	0.0089	-0.1053	0.109	0.1106	-0.0082	0.0222	0.1135	-0.0035	0.0824	79.914	29.612	-13.06
4	4.7856	4.0802	-3.0285	3.5781	-2.8769	4.4036	-0.7261	0.4682	-0.5831	-0.7549	0.383	-0.4668	0.7339	-0.2333	0.3432	0.3238	-0.0619	0.0837	0.1822	-0.042	0.1753	82.767	24.784	-21.631
5	3.9359	2.3311	0.1203	9.2009	0.7745	6.2887	-0.5354	0.7467	0.1614	-1.5367	0.5379	0.1282	-0.1936	-0.0428	-0.0025	0.3872	-0.2237	-0.0388	0.3604	0.0135	0.126	64.49	20.379	-26.911
6	45.1193	-1.2906	-10.3827	8.0095	3.6389	18.7179	-0.3144	1.757	-0.9042	-1.4565	0.0999	-0.5429	0.4381	0.3747	0.2145	0.66	-0.2072	0.0645	0.3562	-0.0953	0.2785	67.117	5.797	-23.802
7	3.2094	-1.1096	1.1717	3.3337	-1.4388	5.5592	-0.0609	-0.004	0.4201	0.1264	0.0055	0.1781	-0.6671	-0.2358	0.0553	0.1789	0.0502	-0.0168	0.1294	-0.0478	0.1707	64.131	37.124	3.146
8	22.9677	1.3779	3.3207	6.2362	2.5682	28.5096	-0.3708	-1.7647	0.155	0.2967	0.3328	0.242	0.7096	1.8974	0.0381	0.1514	0.1191	-0.0522	0.3241	-0.0324	0.0924	77.715	23.4	7.384
9	5.4455	-3.255	0.2782	3.9702	-0.7589	1.4788	-0.123	-0.1417	0.1008	0.1491	0.1538	0.2315	-0.1273	-0.3271	-0.0309	0.1195	0.0106	-0.0277	0.1584	-0.0219	0.1042	63.551	29.694	1.555
10	1.7621	-0.9263	-2.4988	1.3614	0.8981	5.1565	-0.0272	-0.178	0.3606	0.1903	0.1656	-0.2333	-0.4516	-0.0803	-0.1383	0.2501	0.054	-0.0761	0.18	-0.0828	0.2173	69.773	36.351	-0.233
11	18.0056	6.4234	-4.0555	7.0668	-1.2791	8.2063	0.0874	-0.2876	1.6819	0.0823	0.0713	0.9205	-0.6351	-0.2839	-0.1587	0.2779	0.0581	-0.0017	0.1436	0.0257	0.3488	71.86	44.668	-13.863
12	5.0433	-2.7464	7.0718	9.6786	-11.269	24.045	-0.9332	-0.1161	0.7713	0.8422	-0.0282	-0.6749	-1.8424	0.5275	0.9614	0.3456	-0.0489	-0.1132	0.2238	0.0113	0.2762	88.22	40.497	-13.767
13	3.1474	-0.9379	1.3166	6.3903	-1.8405	4.1558	-0.1926	0.1033	-0.0325	-0.1915	0.1577	0.5614	0.0615	-0.5421	0.035	0.1719	-0.1497	-0.0472	0.2201	-0.0107	0.1561	57.2	12.352	-14.394
14	12.2751	18.9995	10.3178	68.0135	40.8997	40.0714	0.478	-0.0126	-0.964	2.048	0.7838	-2.0937	2.5761	0.3948	-1.2617	0.2827	-0.0462	-0.0719	0.1546	0.022	0.2295	70.68	8.289	-0.473
15	2.5841	0.6423	2.944	1.9446	0.2546	6.2343	-0.1796	0.0907	0.0614	-0.3094	0.0337	0.0382	0.3179	-0.263	0.1459	0.1918	-0.1173	-0.0092	0.1455	-0.0103	0.1064	65.229	14.245	-14.495
16	6.673	6.797	4.91	9.7263	5.7692	4.8147	0.251	-0.6264	0.2383	0.3885	-0.3879	0.6207	0.5098	-0.7855	0.1369	0.2132	-0.1463	-0.0223	0.3192	0.0515	0.2219	56.876	11.7	-9.138
17	15.8323	-3.4708	-2.0302	7.4449	1.4104	7.0351	-0.0317	0.3898	-0.1821	-0.387	-0.1482	1.0182	-0.1123	-1.17	0.1799	0.1364	-0.0185	-0.0981	0.3687	-0.0236	0.298	53.015	28.911	-9.189
18	5.045	-1.2632	1.5005	8.8123	-1.1286	11.7153	0.2307	-0.5958	-0.4255	0.5861	0.4014	1.0461	0.0695	-1.5773	-0.6322	0.227	0.0291	0.0993	0.5309	0.0087	0.4234	51.47	29.945	7.197

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	20 - 63
2	X-RAY DIFFRACTION	2	A	64 - 68
3	X-RAY DIFFRACTION	3	A	69 - 84
4	X-RAY DIFFRACTION	4	A	85 - 102
5	X-RAY DIFFRACTION	5	A	103 - 126
6	X-RAY DIFFRACTION	6	A	127 - 135
7	X-RAY DIFFRACTION	7	B	20 - 63
8	X-RAY DIFFRACTION	8	B	64 - 68
9	X-RAY DIFFRACTION	9	B	69 - 86
10	X-RAY DIFFRACTION	10	B	87 - 107
11	X-RAY DIFFRACTION	11	B	108 - 122
12	X-RAY DIFFRACTION	12	B	123 - 135
13	X-RAY DIFFRACTION	13	C	20 - 63
14	X-RAY DIFFRACTION	14	C	64 - 68
15	X-RAY DIFFRACTION	15	C	69 - 85
16	X-RAY DIFFRACTION	16	C	86 - 102
17	X-RAY DIFFRACTION	17	C	103 - 118
18	X-RAY DIFFRACTION	18	C	119 - 135

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