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- PDB-9s4x: AcuB from Geobacillus stearothermophilus with ADP -

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Basic information

Entry
Database: PDB / ID: 9s4x
TitleAcuB from Geobacillus stearothermophilus with ADP
ComponentsAcuB from Geobacillus stearothermophilus
KeywordsDNA BINDING PROTEIN / Repressor / acetoin utilization operon
Function / homologyADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsJanetzky, M. / Palm, G.J. / Lammers, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: AcsA and Acu operon regulation by AcuB
Authors: Janetzky, M. / Palm, G.J. / Lammers, M.
History
DepositionJul 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AcuB from Geobacillus stearothermophilus
B: AcuB from Geobacillus stearothermophilus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,52310
Polymers49,5312
Non-polymers1,9928
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-74 kcal/mol
Surface area19120 Å2
Unit cell
Length a, b, c (Å)52.486, 96.492, 101.088
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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-IDAuth asym-IDLabel asym-ID
1AA
2BB

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

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Components

#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-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-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.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 53 % / Description: thin plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 20000, 100 mM MES pH 6.5, soaked in 10 mM ADP cryo: 10% PEG 20000, 15% PEG 400, 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0596 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0596 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 26470 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 63.7 Å2 / CC1/2: 0.998 / Rsym value: 0.128 / Net I/σ(I): 12.8
Reflection shellResolution: 2.76→3.02 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6233 / CC1/2: 0.906 / Rsym value: 0.527 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
XDSVERSION Jan 19, 2025data reduction
XSCALEVERSION Jan 19, 2025data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→48.293 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 27.063 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R Free: 0.349
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2489 631 4.588 %
Rwork0.1828 13121 -
all0.186 --
obs-13752 99.964 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 70.457 Å2
Baniso -1Baniso -2Baniso -3
1-6.752 Å20 Å20 Å2
2---2.871 Å2-0 Å2
3----3.882 Å2
Refinement stepCycle: LAST / Resolution: 2.76→48.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 124 10 3271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123339
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163252
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.8224567
X-RAY DIFFRACTIONr_angle_other_deg0.5531.7467479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.985399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.504522
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.00554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36910556
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.24310137
X-RAY DIFFRACTIONr_chiral_restr0.0750.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02686
X-RAY DIFFRACTIONr_nbd_refined0.2450.2609
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.23030
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21586
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21906
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.263
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3150.214
X-RAY DIFFRACTIONr_nbd_other0.270.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.22
X-RAY DIFFRACTIONr_mcbond_it4.7955.0341605
X-RAY DIFFRACTIONr_mcbond_other4.7825.0351605
X-RAY DIFFRACTIONr_mcangle_it7.0319.0122001
X-RAY DIFFRACTIONr_mcangle_other7.039.0152002
X-RAY DIFFRACTIONr_scbond_it5.7195.6421734
X-RAY DIFFRACTIONr_scbond_other5.7175.6421735
X-RAY DIFFRACTIONr_scangle_it8.28910.1062566
X-RAY DIFFRACTIONr_scangle_other8.28810.1062567
X-RAY DIFFRACTIONr_lrange_it10.36650.7223471
X-RAY DIFFRACTIONr_lrange_other10.35550.7243470
X-RAY DIFFRACTIONr_ncsr_local_group_10.1080.055697
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.107950.05008
12BX-RAY DIFFRACTIONLocal ncs0.107950.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.76-2.8320.407480.2349290.2429770.9160.9671000.223
2.832-2.9090.253350.2279560.2289910.9520.9691000.213
2.909-2.9930.277500.2238740.2269240.9510.971000.209
2.993-3.0850.319460.1968800.2039260.9230.9771000.181
3.085-3.1850.247390.1938390.1968780.9660.9771000.177
3.185-3.2970.24280.1878450.1888730.9570.9781000.174
3.297-3.420.216340.1857950.1868290.9640.981000.173
3.42-3.5590.226350.1927850.1938200.9640.9781000.183
3.559-3.7170.234250.187390.1827640.9660.981000.173
3.717-3.8970.301330.187070.1857400.9420.981000.173
3.897-4.1060.213340.176740.1727080.9690.9821000.166
4.106-4.3530.224490.1556320.166810.9770.9851000.153
4.353-4.6510.212390.1435900.1476290.9820.9871000.147
4.651-5.020.261300.1435650.1495950.970.9891000.146
5.02-5.4930.248190.1595380.1615570.9690.9851000.162
5.493-6.1320.249150.184840.1824990.9770.9811000.181
6.132-7.0610.325210.2144310.2184520.9470.9741000.217
7.061-8.6030.228330.1583590.1643950.9680.98599.24050.174
8.603-11.9770.17980.1423020.1433100.9860.9891000.16
11.977-48.2930.335100.4171970.4132070.9350.8781000.568
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.98170.9719-1.01433.0753-1.59572.3092-0.0406-0.0430.11480.04120.01710.1298-0.02330.02880.02350.007-0.0015-0.00540.181-0.04860.0671-4.17097.3033-10.0379
20.8585-0.0813-0.09012.62820.20560.5802-0.037-0.04210.19860.16130.01080.21290.1332-0.00210.02620.0390.00820.02650.2101-0.0320.1533-7.67939.6641-3.3784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp2 - 303
2X-RAY DIFFRACTION2ALLBp2 - 303

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