PDB-9s4y: AcuB from Geobacillus stearothermophilus with Ap4A

ID or keywords:

Entry

Database: PDB / ID: 9s4y

Title

AcuB from Geobacillus stearothermophilus with Ap4A

Components

AcuB from Geobacillus stearothermophilus

Keywords

DNA BINDING PROTEIN / Repressor / acetoin utilization operon

Function / homology

BIS(ADENOSINE)-5'-TETRAPHOSPHATE

Function and homology information

Biological species

Bacillus subtilis subsp. subtilis str. 168 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.35 Å

Authors

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

Funding support

1items

Citation

Journal: To Be Published
Title: AcsA and Acu operon regulation by AcuB
Authors: Janetzky, M. / Palm, G.J. / Lammers, M.

History

Deposition	Jul 28, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 25, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9s4y.cif.gz	393.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9s4y.ent.gz	274.6 KB	Display	PDB format
PDBx/mmJSON format	9s4y.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/s4/9s4y ftp://data.pdbj.org/pub/pdb/validation_reports/s4/9s4y	HTTPS FTP

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Related structure data

Related structure data	9s4wC 9s4xC 9s4zC 9s50C 9s51C 9s52C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: AcuB from Geobacillus stearothermophilus

B: AcuB from Geobacillus stearothermophilus

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	52.295, 96.954, 101.709
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 2 - 208 / Label seq-ID: 1 - 207

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	AcuB from Geobacillus stearothermophilus Mass: 24765.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: C-terminal hexa-His-tag Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE Mass: 836.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C₂₀H₂₈N₁₀O₁₉P₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
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: 2.61 Å³/Da / Density % sol: 53 % / Description: thin plate
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% PEG 20000, 100 mM MES pH 6.5, soaked over night in 10 mM Ap4A cryo: 10% PEG 20000, 15% PEG 400, 100 mM MES pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 3.35→50 Å / Num. obs: 7877 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.7 % / B_iso Wilson estimate: 61.2 Å² / CC_1/2: 0.99 / R_sym value: 0.433 / Net I/σ(I): 8
Reflection shell	Resolution: 3.35→50 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1393 / CC_1/2: 0.61 / R_sym value: 1.57 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
XDS	Jun 30, 2024	data reduction
XSCALE	Jun 30, 2024	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.35→48.524 Å / Cor.coef. F_o:F_c: 0.902 / Cor.coef. F_o:F_c free: 0.874 / SU B: 76.22 / SU ML: 0.522 / Cross valid method: THROUGHOUT / ESU R Free: 0.59
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2617	402	5.111 %
R_work	0.2288	7463	-
all	0.231	-	-
obs	-	7865	99.975 %

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: 83.038 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.183 Å²	-0 Å²	0 Å²
2-	-	-3.01 Å²	-0 Å²
3-	-	-	-2.173 Å²

Refinement step

Cycle: LAST / Resolution: 3.35→48.524 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3147	0	108	0	3255

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	3334
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3244
X-RAY DIFFRACTION	r_angle_refined_deg	0.849	1.825	4567
X-RAY DIFFRACTION	r_angle_other_deg	0.309	1.747	7459
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.875	5	400
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.231	5	22
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.284	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.737	10	559
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.017	10	138
X-RAY DIFFRACTION	r_chiral_restr	0.041	0.2	554
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	3761
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	687
X-RAY DIFFRACTION	r_nbd_refined	0.178	0.2	605
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	2961
X-RAY DIFFRACTION	r_nbtor_refined	0.16	0.2	1596
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	1769
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.125	0.2	47
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.162	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.171	0.2	70
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.172	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	1.638	6.041	1606
X-RAY DIFFRACTION	r_mcbond_other	1.638	6.044	1607
X-RAY DIFFRACTION	r_mcangle_it	2.901	10.847	2001
X-RAY DIFFRACTION	r_mcangle_other	2.9	10.849	2002
X-RAY DIFFRACTION	r_scbond_it	1.696	6.363	1728
X-RAY DIFFRACTION	r_scbond_other	1.696	6.363	1728
X-RAY DIFFRACTION	r_scangle_it	3.076	11.658	2565
X-RAY DIFFRACTION	r_scangle_other	3.075	11.656	2566
X-RAY DIFFRACTION	r_lrange_it	5.387	60.812	3452
X-RAY DIFFRACTION	r_lrange_other	5.387	60.822	3453
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.1	0.05	5739

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	0.10045	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.10045	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

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	WR_factor R_work
3.35-3.437	0.386	22	0.341	531	0.343	553	0.879	0.901	0.336
3.437-3.531	0.41	22	0.336	528	0.339	550	0.832	0.915	0.328
3.531-3.633	0.19	17	0.3	520	0.297	537	0.957	0.932	0.288
3.633-3.744	0.297	28	0.28	508	0.28	536	0.911	0.939	0.262
3.744-3.866	0.248	28	0.244	468	0.244	496	0.947	0.958	0.223
3.866-4	0.212	28	0.227	467	0.226	495	0.968	0.964	0.205
4-4.15	0.245	25	0.202	443	0.204	468	0.961	0.972	0.173
4.15-4.319	0.219	31	0.198	432	0.199	463	0.965	0.973	0.174
4.319-4.509	0.239	28	0.182	414	0.186	442	0.96	0.978	0.156
4.509-4.727	0.276	21	0.163	410	0.168	431	0.97	0.983	0.134
4.727-4.98	0.362	18	0.18	377	0.186	395	0.935	0.98	0.151
4.98-5.279	0.195	18	0.181	376	0.181	394	0.978	0.979	0.153
5.279-5.638	0.238	22	0.193	338	0.195	360	0.974	0.977	0.166
5.638-6.083	0.326	25	0.217	321	0.224	346	0.944	0.969	0.191
6.083-6.654	0.259	12	0.276	304	0.275	316	0.964	0.956	0.243
6.654-7.421	0.262	14	0.244	278	0.245	292	0.949	0.959	0.22
7.421-8.536	0.255	13	0.191	244	0.194	257	0.955	0.976	0.175
8.536-10.375	0.201	14	0.153	217	0.156	231	0.989	0.986	0.15
10.375-14.348	0.303	11	0.217	169	0.222	180	0.976	0.978	0.214
14.348-48.524	0.276	5	0.479	118	0.469	123	0.964	0.859	0.471

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	1.1643	1.7816	-1.483	4.7943	-2.4197	3.3313	-0.2032	-0.1196	0.1204	-0.1744	0.1138	0.2009	0.3038	0.0328	0.0893	0.068	-0.0024	-0.0031	0.1332	-0.0405	0.0568	-4.1409	7.2483	-9.8589
2	1.6819	-0.3099	-0.074	4.8715	0.6724	0.9329	-0.0785	-0.2195	0.3842	0.1659	0.0373	0.3159	0.2261	0.0826	0.0412	0.0681	0.0257	0.0114	0.1555	-0.05	0.1379	-6.8427	9.914	-3.7076

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	2 - 301
2	X-RAY DIFFRACTION	2	ALL	Bp	2 - 301

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