PDB-9s50: AcuB from Geobacillus stearothermophilus with AMP and ATP

ID or keywords:

Entry

Database: PDB / ID: 9s50

Title

AcuB from Geobacillus stearothermophilus with AMP and ATP

Components

AcuB from Geobacillus stearothermophilus

Keywords

DNA BINDING PROTEIN / Repressor / acetoin utilization operon

Function / homology

ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Bacillus subtilis subsp. subtilis str. 168 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.06 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	9s50.cif.gz	394 KB	Display	PDBx/mmCIF format
PDB format	pdb9s50.ent.gz	276.3 KB	Display	PDB format
PDBx/mmJSON format	9s50.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/s5/9s50 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/9s50	HTTPS FTP

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Related structure data

Related structure data	9s4wC 9s4xC 9s4yC 9s4zC 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

51.5 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)	51.564, 96.535, 101.435
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)

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Protein , 1 types, 2 molecules AB

#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)

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Non-polymers , 5 types, 14 molecules

#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#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: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.55 Å³/Da / Density % sol: 51.74 % / 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 5 mM AMP + 5 mM ATP 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0596 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2025 / Details: double mirror
Radiation	Monochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0596 Å / Relative weight: 1
Reflection	Resolution: 3.06→50 Å / Num. obs: 10462 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / B_iso Wilson estimate: 84 Å² / CC_1/2: 0.997 / R_sym value: 0.227 / Net I/σ(I): 8.3
Reflection shell	Resolution: 3.06→50 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2027 / CC_1/2: 0.657 / R_sym value: 1.61 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
XDS	VERSION Jan 19, 2025	data reduction
XSCALE	VERSION Jan 19, 2025	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.06→48.314 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.88 / SU B: 69.654 / SU ML: 0.493 / Cross valid method: THROUGHOUT / ESU R Free: 0.525
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2871	513	5.116 %
R_work	0.2232	9514	-
all	0.226	-	-
obs	-	10027	99.741 %

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: 126.787 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	15.027 Å²	0 Å²	0 Å²
2-	-	-6.894 Å²	0 Å²
3-	-	-	-8.133 Å²

Refinement step

Cycle: LAST / Resolution: 3.06→48.314 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3137	0	121	6	3264

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	3333
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3248
X-RAY DIFFRACTION	r_angle_refined_deg	1.099	1.823	4559
X-RAY DIFFRACTION	r_angle_other_deg	0.365	1.746	7469
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.706	5	399
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.498	5	22
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.451	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.111	10	556
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.603	10	137
X-RAY DIFFRACTION	r_chiral_restr	0.049	0.2	553
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3750
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	686
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	619
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	3024
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	1561
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	1789
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	58
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.22	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.225	0.2	58
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.251	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	5.791	10.769	1602
X-RAY DIFFRACTION	r_mcbond_other	5.789	10.77	1603
X-RAY DIFFRACTION	r_mcangle_it	9.226	19.353	1996
X-RAY DIFFRACTION	r_mcangle_other	9.224	19.353	1997
X-RAY DIFFRACTION	r_scbond_it	5.268	11.315	1731
X-RAY DIFFRACTION	r_scbond_other	5.267	11.314	1732
X-RAY DIFFRACTION	r_scangle_it	8.796	20.634	2562
X-RAY DIFFRACTION	r_scangle_other	8.795	20.632	2563
X-RAY DIFFRACTION	r_lrange_it	13.258	109.245	3479
X-RAY DIFFRACTION	r_lrange_other	13.257	109.241	3479
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.095	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	0.09497	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.09497	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
3.06-3.139	0.492	38	0.427	680	0.43	718	0.781	0.817	100	0.436
3.139-3.225	0.408	34	0.408	691	0.408	727	0.813	0.823	99.7249	0.416
3.225-3.318	0.393	35	0.377	634	0.378	669	0.869	0.879	100	0.383
3.318-3.419	0.368	35	0.336	639	0.338	676	0.895	0.886	99.7041	0.337
3.419-3.531	0.381	32	0.319	606	0.321	638	0.881	0.912	100	0.315
3.531-3.654	0.298	27	0.269	607	0.271	639	0.927	0.929	99.2175	0.266
3.654-3.791	0.248	31	0.223	575	0.224	606	0.943	0.96	100	0.21
3.791-3.945	0.235	24	0.208	565	0.209	589	0.953	0.967	100	0.192
3.945-4.119	0.212	24	0.167	532	0.169	556	0.973	0.98	100	0.154
4.119-4.319	0.254	36	0.156	503	0.163	540	0.956	0.984	99.8148	0.145
4.319-4.55	0.217	30	0.148	495	0.152	526	0.978	0.988	99.8099	0.136
4.55-4.824	0.242	17	0.147	472	0.15	489	0.97	0.988	100	0.14
4.824-5.153	0.419	23	0.155	444	0.164	467	0.952	0.989	100	0.148
5.153-5.561	0.3	23	0.152	393	0.159	423	0.962	0.987	98.3452	0.149
5.561-6.083	0.241	22	0.183	388	0.187	410	0.957	0.981	100	0.171
6.083-6.788	0.27	26	0.198	344	0.203	370	0.96	0.978	100	0.19
6.788-7.813	0.212	25	0.182	308	0.184	333	0.977	0.979	100	0.181
7.813-9.506	0.243	11	0.166	277	0.168	289	0.974	0.989	99.654	0.175
9.506-13.191	0.259	15	0.193	213	0.197	231	0.949	0.986	98.7013	0.204
13.191-48.314	0.485	5	0.515	145	0.514	152	0.838	0.876	98.6842	0.7

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	0.6015	0.881	-1.1072	3.0743	-1.788	2.2483	-0.0284	-0.1299	0.0882	-0.0212	-0.0069	0.0519	0.0194	0.1624	0.0354	0.0159	-0.0273	-0.0429	0.2472	-0.0425	0.216	-3.8762	7.2424	-10.1276
2	0.9853	0.297	0.1645	3.4117	0.7677	0.6855	0.0261	-0.1468	0.2791	0.0817	-0.0591	0.2179	0.0605	-0.0175	0.0329	0.0116	0.0064	0.023	0.0705	-0.0305	0.1364	-7.2151	9.4662	-3.3199

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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