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

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Basic information

Entry
Database: PDB / ID: 9s51
TitleAcuB from Geobacillus stearothermophilus with ADP and ATP
ComponentsAcuB from Geobacillus stearothermophilus
KeywordsDNA BINDING PROTEIN / Repressor / acetoin utilization operon
Function / homologyADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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)51,55910
Polymers49,5312
Non-polymers2,0288
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-67 kcal/mol
Surface area18960 Å2
Unit cell
Length a, b, c (Å)52.433, 96.513, 101.157
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

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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 , 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

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Details

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: 52 % / Description: thin plate
Crystal growTemperature: 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

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 PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2025 / Details: double mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0596 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 17740 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Biso Wilson estimate: 67.4 Å2 / CC1/2: 0.999 / Rsym value: 0.17 / Net I/σ(I): 12.4
Reflection shellResolution: 2.53→2.76 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3230 / CC1/2: 0.836 / Rsym value: 1.085 / % possible all: 100

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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
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→48.303 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflection
Rfree0.2434 873 4.922 %
Rwork0.1922 16865 -
all0.195 --
obs-17738 99.921 %
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: 81.911 Å2
Baniso -1Baniso -2Baniso -3
1-5.079 Å20 Å20 Å2
2---1.788 Å20 Å2
3----3.291 Å2
Refinement stepCycle: LAST / Resolution: 2.53→48.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 125 4 3256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123326
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163242
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.8244551
X-RAY DIFFRACTIONr_angle_other_deg0.5691.7467455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.121522
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.07654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22510555
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.63110136
X-RAY DIFFRACTIONr_chiral_restr0.0790.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_nbd_refined0.2310.2571
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22941
X-RAY DIFFRACTIONr_nbtor_refined0.180.21538
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21825
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.242
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3450.215
X-RAY DIFFRACTIONr_nbd_other0.2870.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0750.23
X-RAY DIFFRACTIONr_mcbond_it6.4766.581598
X-RAY DIFFRACTIONr_mcbond_other6.4766.5831599
X-RAY DIFFRACTIONr_mcangle_it9.1411.8151991
X-RAY DIFFRACTIONr_mcangle_other9.13911.8171992
X-RAY DIFFRACTIONr_scbond_it7.2127.1661728
X-RAY DIFFRACTIONr_scbond_other7.2117.1661729
X-RAY DIFFRACTIONr_scangle_it10.19112.9062559
X-RAY DIFFRACTIONr_scangle_other10.18912.9052560
X-RAY DIFFRACTIONr_lrange_it12.43165.1843379
X-RAY DIFFRACTIONr_lrange_other12.4365.1833379
X-RAY DIFFRACTIONr_ncsr_local_group_10.10.055624
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.099550.05008
12BX-RAY DIFFRACTIONLocal ncs0.099550.05008
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
2.53-2.5960.409710.37611930.37812700.8150.84599.52760.377
2.596-2.6660.378730.34611820.34812560.8680.8999.92040.341
2.666-2.7440.332590.32511710.32512310.9050.91199.91880.321
2.744-2.8280.304580.28911090.2911670.920.9271000.277
2.828-2.920.302570.26311200.26511770.9160.9431000.25
2.92-3.0220.285550.25710400.25810950.9430.9521000.239
3.022-3.1360.327570.21310130.21910700.9170.9681000.193
3.136-3.2630.276680.1989810.20310490.9510.9721000.173
3.263-3.4080.271440.29530.2039970.9520.9751000.177
3.408-3.5730.228480.1919190.1939670.970.9781000.172
3.573-3.7650.309420.1718720.1769140.9440.9811000.157
3.765-3.9920.25300.1678340.178640.9670.9821000.155
3.992-4.2660.169360.1387900.1398260.9830.9881000.132
4.266-4.6040.195380.1317250.1347640.9780.98999.86910.131
4.604-5.0390.185490.1256590.1297080.9830.9911000.125
5.039-5.6270.17240.1336310.1356550.9790.991000.134
5.627-6.4820.265170.1955640.1985820.9470.97899.82820.192
6.482-7.9040.189170.1834780.1834960.9770.97999.79840.189
7.904-11.0310.203160.1463920.1484080.9750.9881000.169
11.031-48.3030.293140.3962390.3882540.9430.88499.60630.432
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)
11.13371.1745-1.27863.3288-1.83132.5858-0.0497-0.06720.12710.00560.01420.136-0.04080.01560.03540.0128-0.0027-0.01630.0651-0.03390.0526-4.14227.3409-10.0882
21.1256-0.0656-0.12513.49690.66830.7016-0.0262-0.09960.21080.070.02490.1570.08730.02810.00140.02860.01530.00840.0478-0.02190.058-7.5559.3202-3.2997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp2 - 303
2X-RAY DIFFRACTION2ALLBp2 - 303

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