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- PDB-9qs7: AcuB,Acetoin utilization protein -

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Basic information

Entry
Database: PDB / ID: 9qs7
TitleAcuB,Acetoin utilization protein
ComponentsAcetoin utilization protein AcuB
KeywordsBIOSYNTHETIC PROTEIN / Bacillus subtilis / Acetyl-CoA / Biosynthesis
Function / homology
Function and homology information


acetoin catabolic process / sporulation resulting in formation of a cellular spore
Similarity search - Function
: / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Acetoin utilization protein AcuB
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsZheng, L.J. / Bange, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Structure of AcuB from Bacillus subtilis
Authors: Zheng, L.J. / Bange, G.
History
DepositionApr 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 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: Acetoin utilization protein AcuB
B: Acetoin utilization protein AcuB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5624
Polymers48,8892
Non-polymers1,6732
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-34 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.546, 81.546, 338.549
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Acetoin utilization protein AcuB


Mass: 24444.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: acuB, BSU29700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39066
#2: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE


Mass: 836.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N10O19P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M imidazole (pH 8.0), and 1.0 M potassium/sodium tartrate

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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: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.41→70.62 Å / Num. obs: 26891 / % possible obs: 99.95 % / Redundancy: 36.8 % / Biso Wilson estimate: 82.4 Å2 / CC1/2: 0.999 / Net I/σ(I): 35.04
Reflection shellResolution: 2.411→2.497 Å / Num. unique obs: 2586 / CC1/2: 0.879

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
autoPROC1.1.7 (20210504)data processing
XDSVERSION Jan 10, 2022 BUILT=20220220data scaling
autoPROC1.1.7 (20210504)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→70.62 Å / SU ML: 0.4262 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.6116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2832 1321 4.91 %
Rwork0.2384 25570 -
obs0.2407 26891 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.89 Å2
Refinement stepCycle: LAST / Resolution: 2.41→70.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 106 2 3304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253369
X-RAY DIFFRACTIONf_angle_d0.56344585
X-RAY DIFFRACTIONf_chiral_restr0.0432552
X-RAY DIFFRACTIONf_plane_restr0.0048553
X-RAY DIFFRACTIONf_dihedral_angle_d7.0679432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.510.38091410.33192751X-RAY DIFFRACTION100
2.51-2.620.32581290.30112795X-RAY DIFFRACTION100
2.62-2.760.34481360.31672752X-RAY DIFFRACTION100
2.76-2.930.50761430.39342804X-RAY DIFFRACTION99.97
2.93-3.160.39591550.3372788X-RAY DIFFRACTION99.97
3.16-3.480.33471430.26952810X-RAY DIFFRACTION99.97
3.48-3.980.24291470.23992849X-RAY DIFFRACTION100
3.98-5.010.22181530.19372909X-RAY DIFFRACTION100
5.02-70.620.27991740.21653112X-RAY DIFFRACTION99.85
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)
15.2016343931-1.61096759802-0.8446453895988.02207953745-0.8824102557677.24319491114-0.02057342061350.1001893811990.596190347328-0.451842557375-0.198686382295-0.469661735384-0.6677846197381.471652415960.2137935787940.698499543847-0.216860029727-0.1177462262910.9893147917350.1976757976510.540984840799-15.2151876989-7.74453162274-20.1456444304
28.90216475809-3.33432140129-2.950935296114.500857888931.664657549992.507276771480.515899927450.2954402444871.117495762050.710211972171-0.792254481878-0.245188865159-1.180934765990.4408506610570.04023415898551.79374787986-0.632584558405-0.1825912694571.351052660440.1154146105281.06479211877-15.671909648510.5652612175-18.9678792028
34.327623767960.510319535181-1.545460212714.26662911163-0.6310752034695.36284364295-0.28626595092-0.201404470773-0.1565480135660.5337365514370.00110017400723-0.3663125753560.06873189211051.561963766640.3186391759290.5880433684430.0127735251659-0.03415581081721.064621767580.271032749350.643801077631-15.8294984966-17.8774527302-11.1682541586
47.479885633512.18433804037-0.4320801722298.2642606919-1.216665359579.74625375688-0.237403650167-0.310654640009-0.6138479669590.687341220797-0.03620359806580.3901479007710.698647954853-0.6205620954190.207614480220.654789785422-0.02508650334720.2401210930850.7603264483710.2267286239530.931353884766-34.7966838462-35.62776675712.46572577891
58.63734457859-1.668031274923.051543890660.6831738007840.8065904570397.46362078723-0.705250074166-1.03602742203-1.479871597620.954755210670.1673539734531.020218575272.11768048041-0.9519032379380.68387088021.13079103639-0.1387941755890.4289438749460.9368925224340.1759585412721.27002901217-43.5226139804-39.34212975397.04050587788
68.598127658971.27833567146-3.271405252589.35469875681-0.5304875420538.534378366210.1438623488850.523792474610.844606296659-0.34694567308-0.03140773510380.889568989968-1.17086509434-0.618655716984-0.02686231781520.7403229790130.0629373858892-0.09493958639720.5427786518340.04817861536220.712870917164-38.3723876752-2.14991060635-9.5387376601
76.60953876295-0.0777415432306-1.116217276074.147114153350.884576627328.50850894861-0.06611439331150.714421769504-0.214714866578-0.166612253971-0.1294628962350.805397547998-0.818627338354-0.7830112107210.04711066659010.5113381034480.00754966337205-0.0496532121340.622460506348-0.05412477109210.672674904172-40.2294431503-8.80790777621-14.1599828692
86.92021319853-6.007409812791.759599345617.13164414691-1.098290494784.34812675563-0.612823824577-0.8370081544160.8614508500880.5283381514560.088694299702-0.5086156716350.3717701968220.2905193383090.5286576930230.627081993290.006028541914410.02008332317510.5799842462430.1389190952540.773864346393-32.7045104742-15.863967996-3.03222711657
95.32218920612-1.02867733240.69554720917.541462527630.5854125622526.48495498142-0.164681592427-0.331159005525-1.154558954440.469902194602-0.0321251092552-0.4593271281391.111463024121.082837255920.1480954313580.6679413450630.1646363672160.1533058350670.7826928805940.2594455936740.970446087583-19.0511784613-39.541541595-1.84600867306
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 55 )AA1 - 551 - 55
22chain 'A' and (resid 56 through 76 )AA56 - 7656 - 71
33chain 'A' and (resid 77 through 131 )AA77 - 13172 - 126
44chain 'A' and (resid 132 through 190 )AA132 - 190127 - 185
55chain 'A' and (resid 191 through 206 )AA191 - 206186 - 201
66chain 'B' and (resid 1 through 56 )BC1 - 561 - 56
77chain 'B' and (resid 57 through 112 )BC57 - 11257 - 107
88chain 'B' and (resid 113 through 131 )BC113 - 131108 - 126
99chain 'B' and (resid 132 through 207 )BC132 - 207127 - 202

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