PDB-4avb: Crystal structure of protein lysine acetyltransferase Rv0998 in c...

ID or keywords:

Entry

Database: PDB / ID: 4avb

Title

Crystal structure of protein lysine acetyltransferase Rv0998 in complex with acetyl CoA and cAMP

Components

LYSINE ACETYLTRANSFERASE

Keywords

TRANSFERASE / ALLOSTERIC REGULATION / DOMAIN COUPLING

Function / homology

Function and homology information

acyltransferase activity / acetyltransferase activity / cAMP binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / DNA-binding transcription factor activity / metal ion binding / cytosol
Similarity search - Function

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 1.8 Å

Authors

Lee, H.J. / Lang, P.T. / Fortune, S.M. / Sassetti, C.M. / Alber, T.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Cyclic AMP Regulation of Protein Lysine Acetylation in Mycobacterium Tuberculosis.
Authors: Lee, H.J. / Lang, P.T. / Fortune, S.M. / Sassetti, C.M. / Alber, T.

History

Deposition	May 24, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 11, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 22, 2012	Group: Database references
Revision 1.2	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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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PDBx/mmCIF format	4avb.cif.gz	268.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4avb.ent.gz	218.3 KB	Display	PDB format
PDBx/mmJSON format	4avb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4avb_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	4avb_full_validation.pdf.gz	1.7 MB	Display
Data in XML	4avb_validation.xml.gz	32.5 KB	Display
Data in CIF	4avb_validation.cif.gz	46.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/av/4avb ftp://data.pdbj.org/pub/pdb/validation_reports/av/4avb	HTTPS FTP

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Related structure data

Related structure data	4avaC 4avcC C: citing same article (ref.)
Similar structure data	4avc-1 3sto-d 4avc-2 6bj5-2 4nrv-d 6nl1-d 6dwu-5 5v7b-d 6dwu-29 6dwu-44 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (8) #48 - Dec 2003 Catabolite Activator Protein similarity (8) #251 - Nov 2020 Adenylyl Cyclase similarity (7) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #97 - Jan 2008 Circadian Clock Proteins similarity (3)

Deposited unit

A: LYSINE ACETYLTRANSFERASE

B: LYSINE ACETYLTRANSFERASE

hetero molecules

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

1

A: LYSINE ACETYLTRANSFERASE

hetero molecules

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

2

B: LYSINE ACETYLTRANSFERASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.725, 60.115, 68.240
Angle α, β, γ (deg.)	90.78, 111.71, 114.33
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 2 molecules AB

#1: Protein	LYSINE ACETYLTRANSFERASE Mass: 35661.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O05581

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Non-polymers , 6 types, 510 molecules

#2: Chemical	ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₂N₅O₆P
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula*: C₂₃H₃₈N₇O₁₇P₃S
#6: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.31 Å³/Da / Density % sol: 46.7 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Details: DOUBLE CRYSTAL SI(111)
Radiation	Monochromator: DOUBLE FLAT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.11588 Å / Relative weight: 1
Reflection	Resolution: 1.8→44 Å / Num. obs: 51794 / % possible obs: 87.6 % / Observed criterion σ(I): 3 / Redundancy: 2.9 % / B_iso Wilson estimate: 18.71 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.27 / Mean I/σ(I) obs: 3.2 / % possible all: 87.6

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 1.8→32.123 Å / SU ML: 0.21 / σ(F): 0.02 / Phase error: 21.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2159	2556	5.1 %
R_work	0.1742	-	-
obs	0.1763	50544	81.5 %

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 37.603 Å² / k_sol: 0.33 e/Å³

Displacement parameters

B_iso mean: 25.2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.4218 Å²	-1.9106 Å²	0.7214 Å²
2-	-	-0.3051 Å²	-1.6452 Å²
3-	-	-	-4.1167 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→32.123 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4880	0	217	492	5589

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	5225
X-RAY DIFFRACTION	f_angle_d	1.089	7107
X-RAY DIFFRACTION	f_dihedral_angle_d	14.794	1957
X-RAY DIFFRACTION	f_chiral_restr	0.076	810
X-RAY DIFFRACTION	f_plane_restr	0.005	913

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 (%)
1.8-1.8346	0.3095	140	0.244	2597	X-RAY DIFFRACTION	79
1.8346-1.8721	0.2813	131	0.2248	2611	X-RAY DIFFRACTION	80
1.8721-1.9128	0.261	140	0.1923	2675	X-RAY DIFFRACTION	83
1.9128-1.9573	0.24	143	0.187	2850	X-RAY DIFFRACTION	85
1.9573-2.0062	0.2491	149	0.179	2746	X-RAY DIFFRACTION	84
2.0062-2.0604	0.2075	144	0.168	2729	X-RAY DIFFRACTION	84
2.0604-2.121	0.2065	144	0.1701	2769	X-RAY DIFFRACTION	85
2.121-2.1895	0.2128	179	0.1655	2727	X-RAY DIFFRACTION	84
2.1895-2.2677	0.2179	137	0.1697	2771	X-RAY DIFFRACTION	84
2.2677-2.3585	0.2239	143	0.1802	2728	X-RAY DIFFRACTION	83
2.3585-2.4658	0.2302	119	0.1721	2751	X-RAY DIFFRACTION	83
2.4658-2.5958	0.2551	143	0.184	2700	X-RAY DIFFRACTION	83
2.5958-2.7583	0.2488	162	0.1822	2683	X-RAY DIFFRACTION	82
2.7583-2.9711	0.2509	151	0.1867	2646	X-RAY DIFFRACTION	81
2.9711-3.2699	0.2102	130	0.1776	2616	X-RAY DIFFRACTION	80
3.2699-3.7424	0.2052	140	0.1667	2511	X-RAY DIFFRACTION	77
3.7424-4.7127	0.1634	129	0.1429	2349	X-RAY DIFFRACTION	72
4.7127-32.1283	0.1862	132	0.1722	2529	X-RAY DIFFRACTION	77

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	0.5091	-0.1147	-0.2945	0.1637	-0.1197	0.3864	0.1749	0.1568	0.1874	0.1348	0.0251	0.1777	-0.2373	-0.2797	0.1237	0.1384	0.1883	0.0332	0.2371	0.0358	0.1985	-18.8898	29.0086	-6.6929
2	0.4101	-0.2303	-0.0882	0.2254	-0.1168	0.5246	0.0289	-0.06	0.0803	0.0317	-0.0631	-0.0885	-0.1652	0.0467	0.02	0.1102	0.0014	0.0097	0.0704	0.0116	0.0965	-1.9772	20.4851	-6.6337
3	0.3652	-0.1014	-0.0661	0.2442	-0.0221	0.2509	-0.108	-0.0406	-0.052	0.1174	0.0727	0.0206	0.1465	0.0036	0.0107	0.1233	0.0235	0.024	0.0867	0.0223	0.0913	-2.3864	14.2473	-13.3586
4	0.3018	-0.0331	-0.0117	0.0904	0.1311	0.19	0.0621	0.0198	0.0963	-0.0202	-0.011	0.0126	-0.1769	-0.0395	-0.0268	0.1225	0.0126	0.0248	0.0777	0.0186	0.1147	-5.8885	19.6555	-5.5431
5	1.0858	-0.3041	-0.4361	0.337	0.2466	0.2515	-0.0649	0.1752	-0.202	0.1484	0.1558	0.185	0.0224	-0.1482	-0.057	0.0477	0.0907	0.052	0.0902	-0.0092	0.159	-16.6966	14.1573	-6.815
6	0.1783	0.0138	0.0934	0.3363	0.1702	0.3087	0.0363	-0.0452	0.1079	0.0137	0.0308	-0.228	-0.0014	0.1584	-0.012	0.0895	0.0051	-0.0052	0.118	-0.0169	0.1592	-4.1521	-1.3554	-24.4923
7	0.6912	0.0873	0.1732	0.4002	0.2901	0.5402	0.0217	-0.1211	0.0636	-0.0927	-0.1291	0.0247	-0.1514	-0.0807	0.0642	0.0909	0.0131	0.0051	0.1038	-0.0054	0.1165	-15.5867	1.9545	-28.6544
8	1.3545	-0.0793	-0.713	0.3097	-0.1016	1.0771	0.0705	-0.1746	0.127	0.0673	-0.0287	-0.0136	0.2571	-0.1074	-0.0313	0.0922	-0.0318	0.0135	0.1673	-0.0336	0.1148	-19.0944	-6.2264	-25.652
9	0.3236	0.0068	-0.0036	0.2803	0.1435	0.167	0.1019	-0.1108	-0.0676	0.1619	-0.1547	0.0561	0.2138	-0.1851	0.0039	0.154	-0.0601	-0.0132	0.1776	-0.0016	0.08	-19.705	-10.153	-22.034
10	1.1342	0.5063	-1.0782	1.1206	0.2501	1.9062	0.1428	0.2468	-0.2489	0.0282	-0.0646	-0.0423	0.0789	-0.5228	0.001	0.1833	-0.0558	0.0036	0.2109	0.0019	0.1573	-25.2434	-15.9032	-30.1782
11	0.1049	0.0436	0.016	0.1052	0.1272	0.165	0.0272	0.0311	-0.1766	0.0675	-0.0363	0.0769	0.3095	-0.1509	-0.0423	0.2709	-0.127	-0.0256	0.2423	-0.0247	0.1792	-20.6629	-16.2143	-20.1834
12	1.1493	-0.4682	-0.1037	0.9747	-0.016	0.0208	-0.0552	-0.5187	0.0822	0.4045	0.1228	-0.1442	0.0108	0.3761	-0.0087	0.2136	-0.0314	-0.0271	0.2774	0.0263	0.1238	-8.3011	-6.4117	-10.1267
13	0.8994	-0.1136	0.2447	0.683	0.0322	0.778	0.0967	-0.0606	-0.0332	-0.0277	-0.0377	0.0627	0.1315	-0.0717	0.0275	0.098	-0.0126	-0.024	0.0933	0.0032	0.0928	-9.404	-21.1772	7.2719
14	0.8145	-0.092	-0.3622	0.7165	0.272	1.1989	0.0219	0.0821	-0.0035	-0.0327	-0.0541	0.0206	-0.1754	-0.0145	0.0149	0.1083	-0.0047	0.0086	0.0673	0.004	0.0489	-16.0112	4.2807	24.3976

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 9:41)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 42:70)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 71:88)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 89:114)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 115:142)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 143:170)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 171:226)
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESSEQ 227:248)
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESSEQ 249:277)
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESSEQ 278:297)
11	X-RAY DIFFRACTION	11	CHAIN A AND (RESSEQ 298:314)
12	X-RAY DIFFRACTION	12	CHAIN A AND (RESSEQ 315:332)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 9:142)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 143:333)

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