PDB-9mto: Crystal structure of acetyltransferase CBU0801 from Coxiella burnetii

ID or keywords:

Entry

Database: PDB / ID: 9mto

Title

Crystal structure of acetyltransferase CBU0801 from Coxiella burnetii

Components

[Ribosomal protein bS18]-alanine N-acetyltransferase

Keywords

TRANSFERASE / acetyltransferase / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID

Function / homology

Function and homology information

: / [ribosomal protein bS18]-alanine N-acetyltransferase / protein-N-terminal-alanine acetyltransferase activity / cytoplasm
Similarity search - Function

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.69 Å

Authors

Stogios, P.J. / Evdokimova, E. / Chang, C. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of acetyltransferase CBU0801 from Coxiella burnetii
Authors: Stogios, P.J.

History

Deposition	Jan 11, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9mto.cif.gz	161.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9mto.ent.gz	113.7 KB	Display	PDB format
PDBx/mmJSON format	9mto.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9mto_validation.pdf.gz	1011.2 KB	Display	wwPDB validaton report
Full document	9mto_full_validation.pdf.gz	1017.7 KB	Display
Data in XML	9mto_validation.xml.gz	18.8 KB	Display
Data in CIF	9mto_validation.cif.gz	24.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mt/9mto ftp://data.pdbj.org/pub/pdb/validation_reports/mt/9mto	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
Other databases	TargetTrack: IDP96809

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (5) #97 - Jan 2008 Circadian Clock Proteins similarity (4) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: [Ribosomal protein bS18]-alanine N-acetyltransferase

B: [Ribosomal protein bS18]-alanine N-acetyltransferase

hetero molecules

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

1

A: [Ribosomal protein bS18]-alanine N-acetyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
17.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: [Ribosomal protein bS18]-alanine N-acetyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	41.460, 41.460, 325.720
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Space group name Hall	P3₂2"
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

#1: Protein	[Ribosomal protein bS18]-alanine N-acetyltransferase Mass: 17163.795 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: rimI, CBU_0801 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold References: UniProt: Q83DD7, [ribosomal protein bS18]-alanine N-acetyltransferase
#2: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.37 Å³/Da / Density % sol: 48.08 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.10% w/v n-Octyl-beta-D-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 22% w/v Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.69→46.53 Å / Num. obs: 38359 / % possible obs: 100 % / Redundancy: 11.9 % / B_iso Wilson estimate: 25.29 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.107 / R_pim(I) all: 0.039 / Net I/σ(I): 13.4
Reflection shell	Resolution: 1.69→1.73 Å / Redundancy: 9.9 % / R_merge(I) obs: 1.002 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2775 / CC_1/2: 0.602 / R_pim(I) all: 0.482 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
xia2		data reduction
xia2		data scaling
BALBES		phasing
ARP/wARP		model building
PHENIX		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.69→36.19 Å / SU ML: 0.2026 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3464
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2659	1984	5.19 %
R_work	0.2308	36252	-
obs	0.2327	38236	99.98 %

Solvent computation

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

Displacement parameters

B_iso mean: 42.79 Å²

Refinement step

Cycle: LAST / Resolution: 1.69→36.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2401	0	96	199	2696

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0157	2567
X-RAY DIFFRACTION	f_angle_d	1.8332	3478
X-RAY DIFFRACTION	f_chiral_restr	0.1002	355
X-RAY DIFFRACTION	f_plane_restr	0.0108	431
X-RAY DIFFRACTION	f_dihedral_angle_d	18.922	1039

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 (%)
1.69-1.73	0.3628	155	0.2976	2542	X-RAY DIFFRACTION	99.96
1.73-1.78	0.359	118	0.2822	2499	X-RAY DIFFRACTION	100
1.78-1.83	0.3481	138	0.294	2547	X-RAY DIFFRACTION	100
1.83-1.89	0.3444	149	0.2532	2595	X-RAY DIFFRACTION	100
1.89-1.96	0.2332	133	0.2462	2472	X-RAY DIFFRACTION	99.92
1.96-2.04	0.2527	150	0.2239	2532	X-RAY DIFFRACTION	100
2.04-2.13	0.2706	128	0.2481	2550	X-RAY DIFFRACTION	100
2.13-2.24	0.261	120	0.2239	2602	X-RAY DIFFRACTION	100
2.24-2.38	0.3186	129	0.2398	2565	X-RAY DIFFRACTION	99.93
2.38-2.57	0.2772	125	0.2403	2656	X-RAY DIFFRACTION	100
2.57-2.82	0.2992	147	0.2535	2552	X-RAY DIFFRACTION	99.96
2.82-3.23	0.3026	164	0.2253	2620	X-RAY DIFFRACTION	100
3.23-4.07	0.2258	140	0.2087	2676	X-RAY DIFFRACTION	100
4.07-36.19	0.2356	188	0.2189	2844	X-RAY DIFFRACTION	99.97

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	6.41283867373	0.735804277975	1.64845602464	6.59889109418	4.26117810231	4.30083199809	-0.170035717286	0.36245650063	-0.363900177233	-1.04222176304	-0.124030641537	-0.470798162459	-0.337087610523	0.907842822929	0.198768871508	0.411362424701	-0.0309526296749	0.0330748420424	0.150337039072	0.00942449408576	0.272122300048	17.5917213091	-6.67824425416	-53.528987663
2	4.74959184556	0.0304380001353	0.71753630978	2.27392731724	-0.132599553005	4.36778228571	0.236298324591	-0.301203877921	-0.150584468876	-0.0475902527378	-0.0528190142466	1.07213684193	-0.0847263616897	-0.999729201561	-0.0976102166346	0.126647693822	0.0449284844594	0.00871407348772	0.317132454984	0.0418187339499	0.295796534861	11.8775934053	-11.8723877959	-42.7352591123
3	3.69984807513	1.93942252619	-1.09666742706	3.40635540391	0.101703708172	0.475527018189	0.471216256474	-1.41715968626	0.213550818689	1.35440393083	-0.583281909723	-0.313274111247	-1.14414688936	0.378338399568	-0.0569113262382	0.608673414782	-0.229328828709	0.210591332606	0.479913804879	-0.265865158519	0.138445061628	17.2852081267	-9.23538030476	-35.1726179011
4	4.9360220205	1.31443850927	2.54590457125	3.57583097536	1.13736930559	4.69470443212	-0.273291125688	-0.113222719397	0.40691611303	0.0514566784415	0.12003900417	0.0160965665425	-0.47076640129	0.307296857378	0.153935619893	0.129030826934	-0.0448957962188	-0.0109405804872	0.146058870251	0.00843729849517	0.194477749157	20.4871845225	-8.11008313812	-46.8881659329
5	5.84409917874	-0.0024412676317	0.187642101546	4.22442046994	0.0893759849408	4.10976787553	-0.0662751116885	0.15484651174	0.29006530367	0.227488598023	-0.0314093096206	-0.0553808001678	-0.173930456498	0.432838333669	0.0129498277503	0.114147112711	-0.0205769129434	-0.0114091850692	0.134912991362	0.0443943368737	0.148508144528	25.1884743941	-14.4362280233	-44.9820221836
6	5.01529676982	4.70110335593	-0.779078004336	8.4920218691	-0.0572994203746	0.257504714072	-0.19652337268	1.08226756731	0.803457945635	-0.529027341685	-0.0491944529563	0.138690400414	-0.784905869053	0.706270665571	-0.144657378256	0.27660969846	-0.163352906753	-0.0173797786798	0.350176726457	0.138758840725	0.313832851719	29.7863102399	-7.06395547379	-50.3414181206
7	3.68072321314	1.25429294926	-0.280214239224	6.63467689867	-1.15997405354	3.20185094623	-0.0704696862911	-0.0238350067006	0.449209544251	-0.230528180098	-0.0186127872304	-0.13740222931	-0.415374955584	0.436607894145	0.0462263380809	0.186989887361	-0.0815276595812	-0.0461808438347	0.256391263654	0.0301677229	0.26781663979	32.8201121191	-12.4525028959	-38.385973837
8	4.38972130901	-0.107491751272	-0.157254885176	0.944061463081	-0.760642263227	3.39414181821	-0.0639150594738	-0.66805821341	-0.353658175548	0.0457407617704	-0.222975370713	-0.0340996590059	0.131585531344	0.751802057231	0.233051655455	0.131566444023	0.000701932899013	-0.0040187837168	0.343520699853	0.0511784972097	0.282371590045	30.7104311507	-21.5652775722	-34.0522016926
9	1.86778321184	-0.82925188492	2.33517507301	1.11613325442	0.172603344337	4.86782759567	-0.230567134709	-0.360873107454	0.321821666618	0.0288770420504	-0.115182366125	-0.424679789594	-0.579355920386	0.749304433294	0.279714040348	0.0829323121729	-0.0190185890683	-0.00728380183095	0.492241242579	0.0127360127641	0.305672174915	36.9419042386	-14.3319599978	-39.7684912117
10	0.701441392712	0.045825497333	-0.217412496064	2.11492991732	0.78476552209	0.397465134999	0.252608344014	-0.56014369189	-0.221628558586	0.533480365523	0.224615859683	-0.45647690907	0.111531985144	1.06005108888	-0.00810028664542	0.386385105267	-0.17810766204	-0.165076747287	1.23919748062	-0.097371100668	0.28962590409	21.5917884369	-17.5673123183	-6.74798068057
11	8.04776127487	0.050934772757	1.11259103826	0.596088248308	-1.8683828729	5.98969957672	-0.458181232534	0.0238795163926	1.42788825453	0.0196605486712	0.102861973973	0.226439554337	-1.88510942855	1.44728001931	0.175620982942	0.536941717303	-0.27020104684	-0.0292062930281	0.572205740892	-0.0723385722695	0.546645010807	19.4431926088	-13.1972921503	-16.733873715
12	4.57393371776	1.83483600708	-1.02076288345	3.16203727627	2.25230183066	3.13387527888	0.229705409367	-0.632460509637	0.0940336869521	-0.644198574348	0.503370210009	-0.0249447264977	1.26370329901	-0.110824561043	-0.547935485864	0.62483826288	-0.0468365711596	-0.133748391645	0.972287923552	0.0672011728893	0.292957930157	17.1827006387	-16.9314633329	-2.91064706954
13	3.1725211635	3.90708193229	-0.743502492967	5.53087411347	1.40046632439	7.02679968247	0.366234039967	-0.90573919375	0.0154213764812	0.556034972905	-0.238071569863	0.718676724306	-1.10174288233	-0.483855023376	-0.0280614114394	0.418114498269	-0.00155425561711	-0.0183959625615	0.578471550949	-0.0220628814977	0.217258440066	9.63766664262	-15.0249377887	-10.8260579542
14	2.84320500848	2.31442079151	0.0136386912275	2.04169968021	-0.811318464242	5.01408927761	0.149723712295	-1.4771189059	0.0163774468962	0.916102346628	-0.280878057329	-0.0721082033513	-0.124775541333	-0.158249492044	0.0939947448242	0.579843690074	0.0683707967981	0.0331743508364	0.840470804184	0.00500467847709	0.191464701513	7.05537557131	-19.8345195183	-7.28149858612
15	7.36410675607	-0.615306200127	-4.24246667906	4.53247951977	-0.744577236606	5.7424702547	-0.468214914835	-0.502507346834	-0.817444516577	-0.420222779249	0.42571406478	-0.10442461633	0.791512511966	-0.301053949988	0.0951707061613	0.318411098283	-0.161571407142	5.77573773455E-5	0.416802378094	0.10871580689	0.312669450416	4.82071404641	-28.1060521423	-16.5055760261
16	3.79742689669	1.12501012113	-0.887507495217	2.42974179867	-0.119466494918	5.95172790859	-0.058734165606	-0.313364902891	0.240724489029	0.152491679929	0.109265752043	0.128628056575	-0.174297881336	-0.46912582522	0.01578511581	0.147575518629	0.0283991339002	-0.0259795396924	0.423447527983	0.0762377487187	0.207463814469	3.69181881875	-20.9180008378	-24.1473986087

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid -1 through 7 )	A	A	-1 - 7	1 - 9
2	2	chain 'A' and (resid 8 through 21 )	A	A	8 - 21	10 - 23
3	3	chain 'A' and (resid 22 through 38 )	A	A	22 - 38	24 - 40
4	4	chain 'A' and (resid 39 through 59 )	A	A	39 - 59	41 - 61
5	5	chain 'A' and (resid 60 through 78 )	A	A	60 - 78	62 - 80
6	6	chain 'A' and (resid 79 through 93 )	A	A	79 - 93	81 - 95
7	7	chain 'A' and (resid 94 through 107 )	A	A	94 - 107	96 - 109
8	8	chain 'A' and (resid 108 through 137 )	A	A	108 - 137	110 - 139
9	9	chain 'A' and (resid 138 through 145 )	A	A	138 - 145	140 - 147
10	10	chain 'B' and (resid 1 through 21 )	B	B	1 - 21	1 - 21
11	11	chain 'B' and (resid 22 through 38 )	B	B	22 - 38	22 - 38
12	12	chain 'B' and (resid 39 through 48 )	B	B	39 - 48	39 - 48
13	13	chain 'B' and (resid 49 through 70 )	B	B	49 - 70	49 - 70
14	14	chain 'B' and (resid 71 through 104 )	B	B	71 - 104	71 - 104
15	15	chain 'B' and (resid 105 through 116 )	B	B	105 - 116	105 - 116
16	16	chain 'B' and (resid 117 through 145 )	B	B	117 - 145	117 - 145

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