PDB-9s51: AcuB from Geobacillus stearothermophilus with ADP and ATP

ID or keywords:

Entry

Database: PDB / ID: 9s51

Title

AcuB from Geobacillus stearothermophilus with ADP and ATP

Components

AcuB from Geobacillus stearothermophilus

Keywords

DNA BINDING PROTEIN / Repressor / acetoin utilization operon

Function / homology

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

Function and homology information

Biological species

Bacillus subtilis subsp. subtilis str. 168 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.53 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

-
Download

PDBx/mmCIF format	9s51.cif.gz	399.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9s51.ent.gz	274.2 KB	Display	PDB format
PDBx/mmJSON format	9s51.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s5/9s51 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/9s51	HTTPS FTP

-
Related structure data

Related structure data	9s4vC 9s4wC 9s4xC 9s4yC 9s4zC 9s50C 9s52C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: AcuB from Geobacillus stearothermophilus

B: AcuB from Geobacillus stearothermophilus

hetero molecules

51.6 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)	52.433, 96.513, 101.157
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 (eV)
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)

-
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)

-
Non-polymers , 6 types, 12 molecules

#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-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52 % / 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

-
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	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0596 Å / Relative weight: 1
Reflection	Resolution: 2.53→50 Å / Num. obs: 17740 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.6 % / B_iso Wilson estimate: 67.4 Å² / CC_1/2: 0.999 / R_sym value: 0.17 / Net I/σ(I): 12.4
Reflection shell	Resolution: 2.53→2.76 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3230 / CC_1/2: 0.836 / R_sym value: 1.085 / % possible all: 100

-
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: 2.53→48.303 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.94 / SU B: 33.403 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.458 / ESU R Free: 0.276
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2434	873	4.922 %
R_work	0.1922	16865	-
all	0.195	-	-
obs	-	17738	99.921 %

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: 81.911 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.079 Å²	0 Å²	0 Å²
2-	-	-1.788 Å²	0 Å²
3-	-	-	-3.291 Å²

Refinement step

Cycle: LAST / Resolution: 2.53→48.303 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3127	0	125	4	3256

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	3326
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3242
X-RAY DIFFRACTION	r_angle_refined_deg	1.864	1.824	4551
X-RAY DIFFRACTION	r_angle_other_deg	0.569	1.746	7455
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.2	5	398
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.121	5	22
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.076	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.225	10	555
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.631	10	136
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	553
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3737
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	683
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	571
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	2941
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1538
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	1825
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	42
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.345	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.287	0.2	40
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.075	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	6.476	6.58	1598
X-RAY DIFFRACTION	r_mcbond_other	6.476	6.583	1599
X-RAY DIFFRACTION	r_mcangle_it	9.14	11.815	1991
X-RAY DIFFRACTION	r_mcangle_other	9.139	11.817	1992
X-RAY DIFFRACTION	r_scbond_it	7.212	7.166	1728
X-RAY DIFFRACTION	r_scbond_other	7.211	7.166	1729
X-RAY DIFFRACTION	r_scangle_it	10.191	12.906	2559
X-RAY DIFFRACTION	r_scangle_other	10.189	12.905	2560
X-RAY DIFFRACTION	r_lrange_it	12.431	65.184	3379
X-RAY DIFFRACTION	r_lrange_other	12.43	65.183	3379
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.1	0.05	5624

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	0.09955	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.09955	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
2.53-2.596	0.409	71	0.376	1193	0.378	1270	0.815	0.845	99.5276	0.377
2.596-2.666	0.378	73	0.346	1182	0.348	1256	0.868	0.89	99.9204	0.341
2.666-2.744	0.332	59	0.325	1171	0.325	1231	0.905	0.911	99.9188	0.321
2.744-2.828	0.304	58	0.289	1109	0.29	1167	0.92	0.927	100	0.277
2.828-2.92	0.302	57	0.263	1120	0.265	1177	0.916	0.943	100	0.25
2.92-3.022	0.285	55	0.257	1040	0.258	1095	0.943	0.952	100	0.239
3.022-3.136	0.327	57	0.213	1013	0.219	1070	0.917	0.968	100	0.193
3.136-3.263	0.276	68	0.198	981	0.203	1049	0.951	0.972	100	0.173
3.263-3.408	0.271	44	0.2	953	0.203	997	0.952	0.975	100	0.177
3.408-3.573	0.228	48	0.191	919	0.193	967	0.97	0.978	100	0.172
3.573-3.765	0.309	42	0.171	872	0.176	914	0.944	0.981	100	0.157
3.765-3.992	0.25	30	0.167	834	0.17	864	0.967	0.982	100	0.155
3.992-4.266	0.169	36	0.138	790	0.139	826	0.983	0.988	100	0.132
4.266-4.604	0.195	38	0.131	725	0.134	764	0.978	0.989	99.8691	0.131
4.604-5.039	0.185	49	0.125	659	0.129	708	0.983	0.991	100	0.125
5.039-5.627	0.17	24	0.133	631	0.135	655	0.979	0.99	100	0.134
5.627-6.482	0.265	17	0.195	564	0.198	582	0.947	0.978	99.8282	0.192
6.482-7.904	0.189	17	0.183	478	0.183	496	0.977	0.979	99.7984	0.189
7.904-11.031	0.203	16	0.146	392	0.148	408	0.975	0.988	100	0.169
11.031-48.303	0.293	14	0.396	239	0.388	254	0.943	0.884	99.6063	0.432

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	1.1337	1.1745	-1.2786	3.3288	-1.8313	2.5858	-0.0497	-0.0672	0.1271	0.0056	0.0142	0.136	-0.0408	0.0156	0.0354	0.0128	-0.0027	-0.0163	0.0651	-0.0339	0.0526	-4.1422	7.3409	-10.0882
2	1.1256	-0.0656	-0.1251	3.4969	0.6683	0.7016	-0.0262	-0.0996	0.2108	0.07	0.0249	0.157	0.0873	0.0281	0.0014	0.0286	0.0153	0.0084	0.0478	-0.0219	0.058	-7.555	9.3202	-3.2997

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

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 12 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 6 types, 12 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 12 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi