PDB-9s4v: AcuB from Bacillus subtilis with AMP and ADP

ID or keywords:

Entry

Database: PDB / ID: 9s4v

Title

AcuB from Bacillus subtilis with AMP and ADP

Components

Acetoin utilization protein AcuB

Keywords

PROTEIN BINDING / Repressor / adenine nucleotide / DNA BINDING PROTEIN

Function / homology

Function and homology information

acetoin catabolic process / sporulation resulting in formation of a cellular spore
Similarity search - Function

Biological species

Bacillus subtilis subsp. subtilis str. 168 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.64 Å

Authors

Janetzky, M. / Palm, G.J. / Lammers, M.

Funding support

1items

Citation

Journal: Nat Commun / Year: 2026
Title: AcuB senses cellular energy charge to coordinate acetyl-CoA synthesis in bacteria.
Authors: Janetzky, M. / Geist, N. / Schulze, S. / Ruckert, H. / Gatzemeyer, K. / Palm, G.J. / Berndt, L. / Girbardt, B. / Weis, D. / Menyes, I. / Welsch, N. / Schweder, T. / Dorr, M. / Kemnitz, S. / ...

History

Deposition	Jul 28, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 25, 2026	Provider: repository / Type: Initial release
Revision 1.1	May 20, 2026	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9s4v.cif.gz	624.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9s4v.ent.gz	443.2 KB	Display	PDB format
PDBx/mmJSON format	9s4v.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s4/9s4v ftp://data.pdbj.org/pub/pdb/validation_reports/s4/9s4v	HTTPS FTP

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Related structure data

Related structure data	9s4wC 9s4xC 9s4yC 9s4zC 9s50C 9s51C 9s52C C: citing same article (ref.)
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	#140 - Aug 2011 Rhomboid Protease GlpG similarity (4) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Acetoin utilization protein AcuB

B: Acetoin utilization protein AcuB

C: Acetoin utilization protein AcuB

hetero molecules

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

1

A: Acetoin utilization protein AcuB

B: Acetoin utilization protein AcuB

hetero molecules

defined by author
Evidence: gel filtration
52.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Acetoin utilization protein AcuB

hetero molecules

C: Acetoin utilization protein AcuB

hetero molecules

defined by author
Evidence: gel filtration
52.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	67.305, 79.779, 153.788
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	18
Space group name H-M	P2₁22₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	B
3	2	A
4	2	C
5	3	B
6	3	C

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	HIS	HIS	A	A	0 - 223	1 - 224
2	1	1	HIS	HIS	B	B	0 - 219	1 - 220
3	2	2	TRP	TRP	A	A	0 - 206	1 - 207
4	2	2	TRP	TRP	C	C	0 - 206	1 - 207
5	3	3	TRP	TRP	B	B	0 - 206	1 - 207
6	3	3	TRP	TRP	C	C	0 - 206	1 - 207

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein	Acetoin utilization protein AcuB Mass: 25504.695 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: N-terminal G, C-terminal hexa-His-tag Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: acuB, BSU29700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39066
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.7 Å³/Da / Density % sol: 55 % / Description: block
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: protein (13 mg/mL, with 1 mM AMP) + 5% MPD, 5% ethanol, 100 mM HEPES pH 7.5, cryo: 20% MPD, 5% ethanol, 100 mM HEPES pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.97624 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2024
Radiation	Monochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97624 Å / Relative weight: 1
Reflection	Resolution: 2.64→50 Å / Num. obs: 24477 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 10 % / B_iso Wilson estimate: 73.6 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.063 / R_rim(I) all: 0.145 / R_sym value: 0.137 / Net I/σ(I): 10
Reflection shell	Resolution: 2.64→2.77 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3021 / CC_1/2: 0.64 / R_pim(I) all: 0.8 / R_rim(I) all: 2.602 / R_sym value: 2.437 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
XDS	Jun 30, 2023	data reduction
XSCALE	Jun 30, 2023	data scaling
Aimless	1.13.6	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.64→48.79 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.938 / SU B: 35.485 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R: 0.875 / ESU R Free: 0.344
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2664	1214	4.968 %
R_work	0.2067	23222	-
all	0.209	-	-
obs	-	24436	97.417 %

Solvent computation

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

Displacement parameters

B_iso mean: 100.062 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.31 Å²	-0 Å²	0 Å²
2-	-	6.001 Å²	-0 Å²
3-	-	-	-1.691 Å²

Refinement step

Cycle: LAST / Resolution: 2.64→48.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5096	0	150	14	5260

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	5363
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5218
X-RAY DIFFRACTION	r_angle_refined_deg	1.359	1.827	7290
X-RAY DIFFRACTION	r_angle_other_deg	0.461	1.772	12063
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.884	5	638
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.289	5	28
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.119	5	6
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.598	10	985
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.159	10	217
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	879
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5914
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1082
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	1008
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	4864
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	2575
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2811
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.174	0.2	90
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.01	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.126	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.152	0.2	135
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.159	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	4.661	7.418	2561
X-RAY DIFFRACTION	r_mcbond_other	4.66	7.42	2562
X-RAY DIFFRACTION	r_mcangle_it	7.499	13.336	3193
X-RAY DIFFRACTION	r_mcangle_other	7.498	13.337	3194
X-RAY DIFFRACTION	r_scbond_it	4.859	7.921	2802
X-RAY DIFFRACTION	r_scbond_other	4.859	7.921	2802
X-RAY DIFFRACTION	r_scangle_it	7.915	14.337	4096
X-RAY DIFFRACTION	r_scangle_other	7.914	14.336	4097
X-RAY DIFFRACTION	r_lrange_it	11.391	70.314	5628
X-RAY DIFFRACTION	r_lrange_other	11.39	70.333	5629
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.137	0.05	6084
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.121	0.05	5685
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.118	0.05	5776

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.13658	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.13658	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.12145	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.12145	0.05009
3	5	B	X-RAY DIFFRACTION	Local ncs	0.11789	0.05009
3	6	C	X-RAY DIFFRACTION	Local ncs	0.11789	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.64-2.708	0.393	78	0.363	1487	0.365	1838	0.869	0.862	85.1469	0.364
2.708-2.782	0.353	101	0.329	1660	0.331	1762	0.863	0.9	99.9432	0.321
2.782-2.863	0.388	87	0.319	1635	0.322	1722	0.886	0.913	100	0.313
2.863-2.951	0.336	81	0.286	1607	0.288	1689	0.926	0.931	99.9408	0.278
2.951-3.047	0.329	84	0.274	1542	0.277	1626	0.919	0.942	100	0.259
3.047-3.153	0.318	91	0.235	1474	0.24	1565	0.936	0.956	100	0.218
3.153-3.272	0.253	66	0.223	1462	0.224	1528	0.953	0.966	100	0.207
3.272-3.405	0.308	69	0.215	1396	0.219	1465	0.939	0.969	100	0.197
3.405-3.556	0.288	68	0.216	1118	0.22	1408	0.95	0.969	84.233	0.199
3.556-3.728	0.227	58	0.193	1305	0.195	1363	0.969	0.977	100	0.182
3.728-3.929	0.237	54	0.187	1099	0.189	1291	0.961	0.978	89.3106	0.175
3.929-4.165	0.177	54	0.186	1165	0.186	1219	0.978	0.977	100	0.177
4.165-4.45	0.253	50	0.173	1115	0.176	1165	0.964	0.981	100	0.169
4.45-4.804	0.229	62	0.154	1016	0.158	1079	0.968	0.985	99.9073	0.156
4.804-5.257	0.292	43	0.169	962	0.174	1005	0.96	0.982	100	0.169
5.257-5.869	0.398	38	0.216	858	0.223	896	0.907	0.972	100	0.215
5.869-6.761	0.338	58	0.249	773	0.255	832	0.953	0.966	99.8798	0.25
6.761-8.241	0.246	30	0.184	673	0.187	703	0.972	0.979	100	0.193
8.241-11.492	0.187	30	0.129	541	0.132	572	0.976	0.99	99.8252	0.142
11.492-48.79	0.161	12	0.304	334	0.298	349	0.983	0.926	99.1404	0.463

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	1.7686	-0.9934	-0.3418	1.6899	0.3879	1.0275	-0.0438	0.2739	0.1779	0.1776	-0.0835	0.029	-0.2475	0.0027	0.1272	0.1097	-0.0151	-0.0312	0.0576	0.0459	0.055	27.4207	13.6297	31.6394
2	1.1133	-0.1819	0.3934	1.6853	1.2643	3.1462	-0.1299	0.1015	0.2223	0.0526	0.1168	0.1113	-0.3246	0.241	0.0132	0.0633	-0.0259	0.0054	0.0698	0.0312	0.0764	32.9302	15.0735	33.363
3	3.4322	-0.9009	0.7531	0.2515	-0.3582	2.1476	-0.2236	0.1857	-0.0674	0.1176	-0.0485	-0.0193	-0.5923	0.0601	0.2722	0.2717	-0.0619	-0.1781	0.2373	0.0439	0.1432	5.9612	15.4376	0.0228

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	0 - 302
2	X-RAY DIFFRACTION	2	ALL	Bp	0 - 302
3	X-RAY DIFFRACTION	3	ALL	Cp	0 - 302

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