PDB-9s52: AcuB from Geobacillus stearothermophilus with AMP

ID or keywords:

Entry

Database: PDB / ID: 9s52

Title

AcuB from Geobacillus stearothermophilus with AMP

Components

AcuB from Geobacillus stearothermophilus

Keywords

DNA BINDING PROTEIN / Repressor / acetoin utilization operon

Function / homology

ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Bacillus subtilis subsp. subtilis str. 168 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 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	9s52.cif.gz	404.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9s52.ent.gz	273 KB	Display	PDB format
PDBx/mmJSON format	9s52.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/s5/9s52 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/9s52	HTTPS FTP

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Related structure data

Related structure data	9s4wC 9s4xC 9s4yC 9s4zC 9s50C 9s51C 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
Related items in Molecule of the Month	#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: AcuB from Geobacillus stearothermophilus

B: AcuB from Geobacillus stearothermophilus

hetero molecules

51.2 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)	52.686, 96.414, 101.867
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-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.61 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 30 min in 10 mM AMP 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, 2024 / Details: double mirror
Radiation	Monochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 23740 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.9 % / B_iso Wilson estimate: 41.4 Å² / CC_1/2: 0.996 / R_sym value: 0.276 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.3→2.49 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5002 / CC_1/2: 0.537 / R_sym value: 1.549 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→48.254 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.92 / SU B: 18.963 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.226
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.25	1248	5.259 %
R_work	0.1997	22482	-
all	0.202	-	-
obs	-	23730	99.971 %

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: 45.518 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.02 Å²	0 Å²	0 Å²
2-	-	0.588 Å²	-0 Å²
3-	-	-	-1.608 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→48.254 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3180	0	108	53	3341

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	3366
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3290
X-RAY DIFFRACTION	r_angle_refined_deg	1.747	1.817	4599
X-RAY DIFFRACTION	r_angle_other_deg	0.553	1.743	7569
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.089	5	406
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.737	5	22
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.015	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.552	10	561
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.292	10	138
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	556
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3807
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	697
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	561
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	2908
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1586
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1898
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.199	0.2	65
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.261	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.236	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.217	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.121	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	3.495	3.308	1627
X-RAY DIFFRACTION	r_mcbond_other	3.494	3.31	1628
X-RAY DIFFRACTION	r_mcangle_it	5.479	5.931	2029
X-RAY DIFFRACTION	r_mcangle_other	5.478	5.932	2030
X-RAY DIFFRACTION	r_scbond_it	3.794	3.843	1739
X-RAY DIFFRACTION	r_scbond_other	3.793	3.843	1740
X-RAY DIFFRACTION	r_scangle_it	6.086	6.83	2569
X-RAY DIFFRACTION	r_scangle_other	6.085	6.83	2570
X-RAY DIFFRACTION	r_lrange_it	10.72	38.643	3472
X-RAY DIFFRACTION	r_lrange_other	10.68	38.671	3468
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.101	0.05	5687

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	0.10064	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.10064	0.05008

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
2.3-2.36	0.343	93	0.314	1598	0.316	1695	0.912	0.921	99.764	0.305
2.36-2.424	0.311	83	0.294	1609	0.295	1692	0.92	0.928	100	0.283
2.424-2.494	0.27	85	0.267	1562	0.267	1647	0.955	0.946	100	0.252
2.494-2.571	0.256	83	0.243	1489	0.243	1572	0.955	0.956	100	0.22
2.571-2.655	0.299	81	0.261	1451	0.263	1532	0.936	0.951	100	0.238
2.655-2.748	0.311	57	0.255	1465	0.257	1522	0.933	0.953	100	0.228
2.748-2.851	0.33	86	0.238	1331	0.243	1417	0.928	0.964	100	0.207
2.851-2.967	0.265	70	0.219	1331	0.221	1401	0.944	0.969	100	0.187
2.967-3.098	0.279	63	0.212	1289	0.215	1352	0.945	0.969	100	0.175
3.098-3.249	0.277	67	0.201	1211	0.206	1278	0.952	0.972	100	0.172
3.249-3.424	0.262	64	0.19	1147	0.193	1211	0.954	0.978	100	0.165
3.424-3.63	0.214	62	0.188	1095	0.189	1157	0.975	0.98	100	0.17
3.63-3.879	0.295	61	0.188	1038	0.194	1099	0.948	0.979	100	0.169
3.879-4.188	0.208	62	0.162	962	0.164	1024	0.969	0.983	100	0.145
4.188-4.584	0.186	60	0.137	908	0.141	968	0.981	0.989	100	0.127
4.584-5.12	0.226	38	0.151	812	0.154	850	0.968	0.988	100	0.144
5.12-5.901	0.21	49	0.169	736	0.172	785	0.977	0.985	100	0.157
5.901-7.2	0.242	43	0.17	618	0.175	661	0.962	0.982	100	0.156
7.2-10.071	0.18	24	0.131	515	0.133	539	0.984	0.99	100	0.138
10.071-48.254	0.247	17	0.273	315	0.272	332	0.972	0.946	100	0.292

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	0.6532	0.8699	-0.9432	2.3981	-1.0776	1.6877	-0.0324	0.0127	0.0712	-0.0339	0.0259	0.1374	0.0667	-0.0216	0.0065	0.0925	-0.015	-0.0069	0.0026	0.0016	0.0451	-4.015	7.9586	-10.4608
2	0.5508	-0.1279	-0.0218	2.4489	0.5087	0.5211	-0.0219	0.0202	0.0925	0.0954	-0.0183	0.0328	0.1279	-0.0243	0.0402	0.0714	-0.002	0.009	0.0086	-0.0093	0.0391	-7.7271	9.695	-3.6178

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	2 - 303
2	X-RAY DIFFRACTION	2	ALL	Bp	2 - 303

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