PDB-9s4w: AcuB from Geobacillus stearothermophilus without nucleotide

ID or keywords:

Entry

Database: PDB / ID: 9s4w

Title

AcuB from Geobacillus stearothermophilus without nucleotide

Components

AcuB from Geobacillus stearothermophilus

Keywords

DNA BINDING PROTEIN / Repressor / acetoin utilization operon

Function / homology

TRIETHYLENE GLYCOL

Function and homology information

Biological species

Geobacillus stearothermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 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	9s4w.cif.gz	394.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9s4w.ent.gz	265.1 KB	Display	PDB format
PDBx/mmJSON format	9s4w.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/s4/9s4w ftp://data.pdbj.org/pub/pdb/validation_reports/s4/9s4w	HTTPS FTP

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Related structure data

Related structure data	9s4xC 9s4yC 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

49.8 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)	45.618, 96.777, 98.97
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.) Geobacillus stearothermophilus (bacteria) Gene: AcuB / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#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.: 112 / 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: 2.21 Å³/Da / Density % sol: 44 % / Description: thin plate
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 4041A1 10% PEG 20000, 100 mM MES pH 6.5, 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 PILATUS3 6M / Detector: PIXEL / Date: May 1, 2025
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: 2→50 Å / Num. obs: 30440 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / B_iso Wilson estimate: 35.7 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.031 / R_rim(I) all: 0.113 / R_sym value: 0.109 / Net I/σ(I): 20.7
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2219 / CC_1/2: 0.82 / R_pim(I) all: 0.338 / R_rim(I) all: 1.224 / R_sym value: 1.176 / % 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: 2→48.435 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.929 / SU B: 10.969 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.169
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2447	1465	4.822 %
R_work	0.1906	28917	-
all	0.193	-	-
obs	-	30382	99.977 %

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: 38.967 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.558 Å²	-0 Å²	0 Å²
2-	-	-1.932 Å²	0 Å²
3-	-	-	-1.626 Å²

Refinement step

Cycle: LAST / Resolution: 2→48.435 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3190	0	16	112	3318

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	3276
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3251
X-RAY DIFFRACTION	r_angle_refined_deg	1.91	1.824	4456
X-RAY DIFFRACTION	r_angle_other_deg	0.614	1.749	7474
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.407	5	402
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	16.014	5	22
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.951	10	560
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.777	10	140
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	535
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3750
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	686
X-RAY DIFFRACTION	r_nbd_refined	0.238	0.2	624
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	3110
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	1592
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	1948
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.186	0.2	123
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.131	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.171	0.2	55
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.153	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	3.202	2.926	1623
X-RAY DIFFRACTION	r_mcbond_other	3.201	2.928	1624
X-RAY DIFFRACTION	r_mcangle_it	4.772	5.214	2020
X-RAY DIFFRACTION	r_mcangle_other	4.772	5.217	2021
X-RAY DIFFRACTION	r_scbond_it	4.232	3.577	1653
X-RAY DIFFRACTION	r_scbond_other	4.23	3.578	1654
X-RAY DIFFRACTION	r_scangle_it	6.512	6.284	2436
X-RAY DIFFRACTION	r_scangle_other	6.511	6.284	2437
X-RAY DIFFRACTION	r_lrange_it	8.743	32.405	3478
X-RAY DIFFRACTION	r_lrange_other	8.737	32.401	3464
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.142	0.05	5573

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	0.14216	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.14216	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
2-2.052	0.303	100	0.29	2115	0.291	2215	0.9	0.919	100	0.255
2.052-2.108	0.289	100	0.259	2038	0.26	2138	0.931	0.935	100	0.224
2.108-2.169	0.264	117	0.234	1988	0.236	2105	0.946	0.952	100	0.199
2.169-2.236	0.258	84	0.212	1940	0.214	2024	0.943	0.963	100	0.172
2.236-2.309	0.254	84	0.189	1894	0.192	1978	0.957	0.97	100	0.153
2.309-2.39	0.247	114	0.2	1807	0.202	1921	0.956	0.969	100	0.161
2.39-2.48	0.33	83	0.2	1762	0.205	1845	0.932	0.97	100	0.162
2.48-2.581	0.273	72	0.201	1701	0.204	1773	0.953	0.972	100	0.167
2.581-2.695	0.257	75	0.205	1659	0.207	1736	0.962	0.974	99.8848	0.169
2.695-2.826	0.265	93	0.19	1533	0.195	1627	0.962	0.976	99.9385	0.16
2.826-2.978	0.255	88	0.208	1485	0.21	1573	0.96	0.972	100	0.175
2.978-3.158	0.289	64	0.193	1410	0.197	1474	0.956	0.976	100	0.168
3.158-3.375	0.25	63	0.21	1348	0.212	1411	0.956	0.973	100	0.188
3.375-3.644	0.281	76	0.187	1237	0.193	1314	0.955	0.978	99.9239	0.173
3.644-3.99	0.206	55	0.165	1150	0.167	1205	0.977	0.983	100	0.156
3.99-4.457	0.171	59	0.14	1054	0.142	1113	0.985	0.988	100	0.135
4.457-5.139	0.249	48	0.153	942	0.156	990	0.967	0.987	100	0.15
5.139-6.277	0.248	49	0.195	794	0.198	843	0.968	0.981	100	0.186
6.277-8.803	0.175	29	0.164	656	0.164	685	0.973	0.985	100	0.164
8.803-48.435	0.123	12	0.186	404	0.184	417	0.984	0.976	99.7602	0.196

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	0.2476	0.3729	-0.4232	1.0141	-0.8091	1.18	0.0047	-0.0274	0.0275	0.0627	-0.0259	0.0159	-0.0395	0.0191	0.0213	0.042	0.0083	0.0244	0.0076	-0.0014	0.0369	-2.1864	6.8996	-9.227
2	0.135	-0.3069	-0.174	1.7979	0.7111	0.8874	0.0288	-0.0134	0.0401	0.0167	0.0016	-0.0609	-0.0005	-0.0159	-0.0304	0.0145	-0.0015	0.0111	0.0234	-0.0287	0.0573	-4.3285	7.7464	-2.8301

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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