PDB-9cr5: Crystal structure of GNAT superfamily acetyltransferase PA2271 fr...

ID or keywords:

Entry

Database: PDB / ID: 9cr5

Title

Crystal structure of GNAT superfamily acetyltransferase PA2271 from Pseudomonas aeruginosa

Components

Acetyltransferase PA2271

Keywords

TRANSFERASE / GNAT / acetyltransferase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

acyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / Acetyltransferase PA2271

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.56 Å

Authors

Majorek, K.A. / Cooper, D.R. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)

Funding support

United States, 1items

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural, functional, and regulatory evaluation of a cysteine post-translationally modified Gcn5-related N-acetyltransferase.
Authors: Uychoco, P. / Majorek, K.A. / Ives, A.N. / Le, V.T.B. / Caro De Silva, P.L. / Paurus, V.L. / Attah, I.K. / Lipton, M.S. / Minor, W. / Kuhn, M.L.

History

Deposition	Jul 20, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 28, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9cr5.cif.gz	194.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9cr5.ent.gz	137.1 KB	Display	PDB format
PDBx/mmJSON format	9cr5.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/cr/9cr5 ftp://data.pdbj.org/pub/pdb/validation_reports/cr/9cr5	HTTPS FTP

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Related structure data

Similar structure data	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
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: Acetyltransferase PA2271

B: Acetyltransferase PA2271

hetero molecules

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

1

A: Acetyltransferase PA2271

hetero molecules

defined by author
20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Acetyltransferase PA2271

hetero molecules

defined by author
20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	128.407, 131.110, 44.721
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-202- NA
2	1	A-459- HOH
3	1	B-485- HOH
4	1	B-505- HOH

#1: Protein	Acetyltransferase PA2271 / GCN5-related N-acetyltransferase / GNAT Mass: 19566.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA2271 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9I1K2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical	ChemComp-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₃H₃₈N₇O₁₇P₃S / Feature type*: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.17 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M calcium chloride, 100 mM Tris pH 8.0, 20% PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2012 / Details: Beryllium Lenses
Radiation	Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 1.56→50 Å / Num. obs: 53569 / % possible obs: 99.9 % / Redundancy: 8.5 % / B_iso Wilson estimate: 26.29 Å² / R_merge(I) obs: 0.114 / R_pim(I) all: 0.041 / R_rim(I) all: 0.122 / Χ²: 1.091 / Net I/av σ(I): 12.55 / Net I/σ(I): 12.5
Reflection shell	Resolution: 1.57→1.6 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.25 / Num. unique obs: 2666 / CC_1/2: 0.738 / CC star: 0.922 / R_pim(I) all: 0.349 / R_rim(I) all: 0.956 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
HKL-3000		data scaling
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.56→25.24 Å / SU ML: 0.1809 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.0405
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2015	2727	5.09 %
R_work	0.1668	50816	-
obs	0.1685	53543	98.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 33.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.56→25.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2709	0	109	497	3315

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0091	3038
X-RAY DIFFRACTION	f_angle_d	1.0889	4152
X-RAY DIFFRACTION	f_chiral_restr	0.0628	435
X-RAY DIFFRACTION	f_plane_restr	0.0069	550
X-RAY DIFFRACTION	f_dihedral_angle_d	26.6569	1140

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.56-1.59	0.2658	122	0.2452	2191	X-RAY DIFFRACTION	81.79
1.59-1.62	0.2793	148	0.2314	2655	X-RAY DIFFRACTION	99.86
1.62-1.65	0.2498	130	0.2187	2676	X-RAY DIFFRACTION	99.89
1.65-1.69	0.2819	163	0.2083	2630	X-RAY DIFFRACTION	99.96
1.69-1.73	0.2314	140	0.2042	2712	X-RAY DIFFRACTION	100
1.73-1.77	0.2333	148	0.2049	2613	X-RAY DIFFRACTION	99.89
1.77-1.82	0.2596	140	0.1923	2697	X-RAY DIFFRACTION	100
1.82-1.87	0.2149	159	0.1883	2672	X-RAY DIFFRACTION	99.96
1.87-1.93	0.2707	131	0.1865	2699	X-RAY DIFFRACTION	99.96
1.93-2	0.2498	145	0.1876	2681	X-RAY DIFFRACTION	99.96
2-2.08	0.2181	146	0.1843	2680	X-RAY DIFFRACTION	100
2.08-2.18	0.2074	150	0.177	2680	X-RAY DIFFRACTION	100
2.18-2.29	0.204	137	0.1668	2711	X-RAY DIFFRACTION	100
2.29-2.44	0.2089	164	0.1701	2678	X-RAY DIFFRACTION	100
2.44-2.62	0.1838	150	0.1706	2735	X-RAY DIFFRACTION	99.9
2.62-2.89	0.1851	130	0.1708	2694	X-RAY DIFFRACTION	99.96
2.89-3.3	0.183	126	0.1666	2777	X-RAY DIFFRACTION	99.9
3.3-4.16	0.2098	140	0.1439	2765	X-RAY DIFFRACTION	99.76
4.16-25.24	0.1691	158	0.1514	2870	X-RAY DIFFRACTION	99.51

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	5.98954072882	-5.34892091686	2.31022880936	5.39067296139	-1.01393335017	6.57867957504	-0.377978381172	0.570153548474	0.684587203498	-1.67444154189	0.210544947881	-0.343283472458	-0.956184300581	0.561374001453	0.11909120668	0.484078661558	-0.052762605364	0.0363531556601	0.321757923618	0.0478018162207	0.206314989445	-38.4292950302	20.2205912906	-20.1937106294
2	7.19739511014	1.88501742185	4.77892578035	4.38460495696	2.24408000017	3.41655817487	0.159918224269	0.246341958921	-0.142151416015	-0.285292991561	0.0952186348287	-0.145878851728	0.066380915844	0.262275940998	-0.216791838309	0.168150298691	0.0189814665994	0.0212529191197	0.158011536388	0.030248862657	0.150162962324	-32.9301545201	8.86724088361	-9.5085058677
3	2.89728266446	-0.636599707625	2.58122911339	3.84854738513	-2.33484110102	3.07277042483	0.450367030032	-0.545238524405	-0.230919189315	0.384596084901	-0.204022392411	-0.272353783879	0.794568950476	-0.447591798976	-0.126412265598	0.238289135082	-0.0839860834562	-0.0302540940913	0.328253012921	0.0552746316881	0.152596672272	-33.2543639912	6.04440134694	2.44752376207
4	3.14860756434	-1.26586157261	-2.90985033172	4.6162731957	-0.0634530649533	3.08791971606	-0.250819886192	0.289164119418	-0.617050071235	-0.599552977451	-0.112165047344	0.805125196894	0.551811008711	-0.606679286178	0.404889115507	0.410219508287	-0.00758859762152	-0.0715153753305	0.267317230444	-0.0275943384968	0.291978597981	-46.5141096271	3.95016878921	-16.8956782212
5	8.57935147491	3.42256832799	0.0254879816009	8.3887819149	-0.299567997889	4.31621672359	-0.136523914901	0.725017304919	0.172948521078	-1.19771478992	0.0976827386387	-0.276202295522	-0.0969646545036	0.383681379199	0.0498452126875	0.437009665838	0.0082509106562	-0.0102063974763	0.291560292329	0.0567565976033	0.153516479123	-38.0295995978	16.7196841238	-18.8512034736
6	9.04158189853	0.212103565662	1.1029935512	3.60892108628	0.0489986642408	1.07760117865	-0.0717262599298	0.00272869105813	0.319395882798	-0.204912011709	-0.00817628594064	0.319060246854	-0.0907081034006	-0.0390266033163	0.082359103085	0.189967705648	0.00132486779863	-0.0422076428916	0.164894042041	0.0108418393818	0.136169519637	-44.6018198213	17.5702356635	-10.0255798904
7	8.97269920066	-1.62452179253	5.91232064345	3.21522184281	-1.31906562683	6.38739723802	-0.0664522381225	-0.181231568045	0.255182783033	0.0583033040398	-0.0244126836323	0.449594903107	-0.090720161909	-0.23194336204	0.126805058379	0.133478158184	0.0118023134485	0.00788191007529	0.16402434295	0.00883592008303	0.213545517873	-48.0738169556	15.8779925635	-0.655044897089
8	6.36999646436	5.41950027716	-2.06474522118	8.87431764372	-3.0639770268	6.54821045955	-0.0889280507578	-0.0442269925774	0.424628671596	0.809825263793	0.206022591315	0.722439096386	-0.0881036843533	0.0314930869142	-0.133644605078	0.276962733465	0.0443329662283	0.0481492808212	0.211777096498	0.00290926838759	0.28181936461	-48.595164752	20.5154066907	3.32409763605
9	3.35769549514	-1.57581862984	0.704122984616	6.60723514433	-0.906340048484	2.20667847334	-0.12772539878	-0.149724881028	-0.136013247731	0.598022124575	0.174491240206	0.741761510243	-0.0106723707768	-0.201901686059	-0.0508922294499	0.244952761531	0.00501460727073	0.0739326204988	0.246130218228	0.0262734813351	0.274682873807	-51.050653015	8.60939546755	4.38483653491
10	4.30357406656	0.493729559043	0.894799370914	5.48832962991	3.17910821114	8.09666160929	0.00848382892709	0.468268277836	0.156663420391	-0.493879907415	0.144721292669	0.0872708466381	-0.0981357922433	0.0990558241909	-0.186056150223	0.225425416017	8.75925892789E-5	0.000451708284809	0.217613577799	0.0521585632095	0.180125823097	-14.3517151906	28.4447698165	-3.6609268995
11	4.89076197528	-5.30042221029	-5.89367963353	5.77761956543	6.47315451061	7.28628419837	0.0765753001013	-0.095638512622	0.717932413625	0.340850649795	0.148296074625	-0.703373289249	0.192535361409	0.186926166687	-0.249738859363	0.261200507598	-0.00923811317861	-0.0187037744478	0.237461003959	-0.0322164728601	0.316105111147	-9.70168148403	34.1542101851	16.5574626797
12	5.71840742095	1.06671729204	1.51976431687	3.63841505919	-0.320600021759	5.97888259308	-0.286111279327	0.781580959294	0.0535614731123	-0.470581036679	0.219286388672	-0.187432056209	0.0169590045718	0.374613344165	0.0512142129539	0.29719573429	-0.0285352312985	0.0310475479482	0.27388908172	0.0175204728967	0.140600916828	-9.4660607933	22.8879854648	-5.36705859619
13	3.29521854187	0.00171586522071	0.878390881158	2.78863281742	-0.611944158777	1.68656483946	0.0394955469597	0.0707356832248	-0.00730155365859	0.16646540537	0.0616494996857	0.104180896889	-0.0389741387129	-0.0501911710927	-0.0717150655675	0.214181752186	0.00159234185097	0.0208031503012	0.218415379556	-0.0125118577871	0.167509432477	-17.7195552947	19.5346126027	1.38332033298
14	3.93989197279	1.54175358804	2.39894866976	8.83091298831	5.6349150536	5.96137124582	0.067131943252	-0.260881909597	0.108173373893	0.300967986603	-0.0063159661641	0.09664172424	0.162376727239	-0.0934286911197	-0.0200209410937	0.184518233986	-0.0168617029283	-0.0054933346596	0.206809429475	0.0287905894876	0.192455833467	-15.5919290902	16.3504631724	10.7795189583
15	7.72996643183	-4.43999618837	5.17817039302	6.47444588745	-3.14776441848	3.50764179946	0.140852773306	-0.982637493856	0.0195082602888	0.427215289778	0.0196949482635	0.110075366867	0.188022881419	-0.415917402445	-0.136579167513	0.26373653171	-0.0534012346251	0.0197320539677	0.35884812703	-0.0094245027187	0.174169283668	-20.1494177616	15.4257929831	14.8158078357
16	8.21455790391	3.44858940782	2.16397505022	3.48094277611	1.29979704468	2.31185609028	0.39618087811	-0.428017388403	-0.170491634796	0.398571681496	-0.205081103359	-0.026441102336	0.49960884332	-0.0700278860891	-0.213749763225	0.306202341358	0.0164415395561	-0.0563072384076	0.268914668784	0.0184496339209	0.190334368178	-8.05950152947	13.763136127	15.7458766304

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 9 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 29 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 30 through 43 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 44 through 53 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 54 through 65 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 66 through 109 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 110 through 126 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 127 through 139 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 140 through 172 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 27 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 28 through 38 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 39 through 65 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 66 through 109 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 110 through 126 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 127 through 139 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 140 through 173 )

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Yorodumi