PDB-4ubr: Crystal structure of Pseudomonas aeruginosa N-aetyltransferase PA4534

ID or keywords:

Entry

Database: PDB / ID: 4ubr

Title

Crystal structure of Pseudomonas aeruginosa N-aetyltransferase PA4534

Components

Putative acetyltransferase

Keywords

TRANSFERASE / N-acetyltransferase superfamily / Pseudomonas aeruginosa / GNAT family

Function / homology

Function and homology information

N-acetyltransferase activity
Similarity search - Function

Biological species

Pseudomonas aeruginosa 18A (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.21 Å

Authors

Choe, J. / Shin, S.

Citation

Journal: To Be Published
Title: Crystal structure of Pseudomonas aeruginosa N-aetyltransferase PA4534
Authors: Choe, J.

History

Deposition	Aug 13, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Aug 19, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ubr.cif.gz	502.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ubr.ent.gz	420 KB	Display	PDB format
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Validation report

Summary document	4ubr_validation.pdf.gz	516.8 KB	Display	wwPDB validaton report
Full document	4ubr_full_validation.pdf.gz	537.9 KB	Display
Data in XML	4ubr_validation.xml.gz	53.7 KB	Display
Data in CIF	4ubr_validation.cif.gz	73.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ub/4ubr ftp://data.pdbj.org/pub/pdb/validation_reports/ub/4ubr	HTTPS FTP

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Related structure data

Similar structure data	5ib0-2 5ib0-3 5ib0-1 5ib0-4 1os0-d 1y7r-d 6hiu-d 5i84-6 5i84-7 5v3w-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #97 - Jan 2008 Circadian Clock Proteins similarity (4)

Deposited unit

A: Putative acetyltransferase

B: Putative acetyltransferase

C: Putative acetyltransferase

D: Putative acetyltransferase

E: Putative acetyltransferase

F: Putative acetyltransferase

G: Putative acetyltransferase

H: Putative acetyltransferase

I: Putative acetyltransferase

hetero molecules

144 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative acetyltransferase

B: Putative acetyltransferase

hetero molecules

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

2

C: Putative acetyltransferase

D: Putative acetyltransferase

hetero molecules

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

3

E: Putative acetyltransferase

F: Putative acetyltransferase

hetero molecules

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

4

G: Putative acetyltransferase

H: Putative acetyltransferase

hetero molecules

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

5

I: Putative acetyltransferase

hetero molecules

I: Putative acetyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	137.367, 137.367, 200.854
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Putative acetyltransferase Mass: 15938.206 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa 18A (bacteria) / Gene: PA18A_479 / Production host: Escherichia coli (E. coli) / References: UniProt: M1Y000, UniProt: A0A0M3KKY2*PLUS
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 589 / 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: 3.39 Å³/Da / Density % sol: 63.68 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Calcium acetate, 0.1M Tris HCl pH 7.0, 16% PEG 1000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.21→50 Å / Num. obs: 96199 / % possible obs: 99.6 % / Redundancy: 15 % / Net I/σ(I): 21.9

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Processing

Software

Name: REFMAC / Version: 5.8.0049 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.21→24.7 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.942 / SU B: 9.739 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22763	4806	5 %	RANDOM
R_work	0.19207	-	-	-
obs	0.19387	91142	99.69 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 33.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.18 Å²	-0 Å²	0 Å²
2-	-	-0.18 Å²	0 Å²
3-	-	-	0.35 Å²

Refinement step

Cycle: 1 / Resolution: 2.21→24.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9855	0	66	589	10510

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	10126
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9822
X-RAY DIFFRACTION	r_angle_refined_deg	1.739	1.957	13663
X-RAY DIFFRACTION	r_angle_other_deg	0.863	3	22330
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.322	5	1224
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.278	21.404	513
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.158	15	1674
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.872	15	144
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	1460
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	11475
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2601
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	2.858	3.02	4923
X-RAY DIFFRACTION	r_mcbond_other	2.858	3.02	4922
X-RAY DIFFRACTION	r_mcangle_it	4.059	4.513	6138
X-RAY DIFFRACTION	r_mcangle_other	4.059	4.513	6139
X-RAY DIFFRACTION	r_scbond_it	3.819	3.547	5203
X-RAY DIFFRACTION	r_scbond_other	3.818	3.547	5203
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.89	5.119	7525
X-RAY DIFFRACTION	r_long_range_B_refined	8.361	25.12	11724
X-RAY DIFFRACTION	r_long_range_B_other	8.337	24.873	11558
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.211→2.268 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.26	339	-
R_work	0.232	6580	-
obs	-	-	99.63 %

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	0.0418	-0.1224	0.0893	0.3674	-0.2761	0.2259	-0.0338	-0.0063	0.0086	0.0812	-0.0059	-0.036	-0.0031	0.0303	0.0397	0.2117	0.0903	0.0101	0.0888	0.0136	0.038	167.064	29.91	18.656
2	1.0278	-0.2994	-0.3893	0.8399	0.1753	0.3466	-0.0383	-0.0118	-0.0645	0.1818	-0.0905	0.1237	0.0382	-0.0279	0.1287	0.0859	0.0237	0.0229	0.0621	-0.0321	0.0651	146.382	40.956	9.486
3	0.1386	0.4808	-0.0668	1.8236	0.0296	1.3691	-0.0246	-0.0013	0.097	-0.007	-0.036	0.4115	-0.037	-0.4501	0.0605	0.0587	0.0441	0.0293	0.2025	-0.0147	0.1543	181.438	15.592	63.223
4	1.256	-0.1841	0.1669	0.3192	-0.3074	0.5542	-0.0658	-0.0164	0.2652	0.0937	-0.0467	0.0404	-0.3613	0.059	0.1124	0.3296	0.0029	-0.1287	0.0442	0.0061	0.1747	194.218	34.524	52.331
5	0.9804	0.3543	-0.5637	0.3646	0.2698	1.2866	-0.0783	0.1712	0.1337	-0.04	0.0967	0.0805	0.0131	-0.0768	-0.0184	0.0547	0.0184	-0.0159	0.1044	0.0627	0.0541	148.37	56.283	78.313
6	1.0388	0.1653	0.6616	0.3408	0.1212	1.0232	-0.0992	0.2271	-0.2027	0.0103	0.0773	-0.1253	0.232	0.2282	0.0219	0.1683	0.0343	0.08	0.1448	-0.0292	0.1148	156.187	32.456	77.502
7	1.397	0.6638	0.1932	1.3432	0.2647	1.2033	-0.1382	0.2277	0.3236	-0.3177	0.1114	0.1655	-0.0981	0.0392	0.0269	0.1462	-0.0184	-0.0095	0.0904	0.0724	0.0902	191.698	6.773	28.508
8	3.1778	0.1012	0.3184	1.3803	-0.1503	0.6125	0.0058	0.3643	0.0954	-0.2885	0.0233	0.377	0.0672	-0.1424	-0.0291	0.0997	-0.0062	-0.0683	0.1663	0.0223	0.134	169.277	-3.36	34.444
9	0.919	-0.2388	0.4337	0.4524	-0.3304	1.126	-0.1893	0.0431	0.237	0.1964	0.0019	-0.1637	-0.4396	0.0694	0.1874	0.2873	0.0714	-0.0915	0.1308	0.0143	0.145	172.41	51.229	105.6

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 137
2	X-RAY DIFFRACTION	2	B	1 - 137
3	X-RAY DIFFRACTION	3	C	1 - 137
4	X-RAY DIFFRACTION	4	D	1 - 137
5	X-RAY DIFFRACTION	5	E	1 - 137
6	X-RAY DIFFRACTION	6	F	1 - 137
7	X-RAY DIFFRACTION	7	G	1 - 137
8	X-RAY DIFFRACTION	8	H	1 - 137
9	X-RAY DIFFRACTION	9	I	1 - 137

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