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- PDB-9vlh: Crystal structure of Bacillus subtilis DegQ tetramer -

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Basic information

Entry
Database: PDB / ID: 9vlh
TitleCrystal structure of Bacillus subtilis DegQ tetramer
ComponentsDegradation enzyme regulation protein DegQ
KeywordsTRANSCRIPTION / transcription regulatory protein
Function / homologyDegradation enzyme regulation protein DegQ / DegQ (SacQ) family / positive regulation of single-species biofilm formation / Degradation enzyme regulation protein DegQ
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.3 Å
AuthorsFujimoto, Z. / Kishine, N. / Kimura, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Tetrameric structure of Bacillus subtilis DegQ and its predicted interaction with the DegS-DegU two-component system.
Authors: Fujimoto, Z. / Kishine, N. / Saitou, K. / Kimura, K.
History
DepositionJun 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Degradation enzyme regulation protein DegQ
B: Degradation enzyme regulation protein DegQ
C: Degradation enzyme regulation protein DegQ
D: Degradation enzyme regulation protein DegQ
E: Degradation enzyme regulation protein DegQ
F: Degradation enzyme regulation protein DegQ
G: Degradation enzyme regulation protein DegQ
H: Degradation enzyme regulation protein DegQ


Theoretical massNumber of molelcules
Total (without water)44,4448
Polymers44,4448
Non-polymers00
Water1,54986
1
A: Degradation enzyme regulation protein DegQ
B: Degradation enzyme regulation protein DegQ
C: Degradation enzyme regulation protein DegQ
D: Degradation enzyme regulation protein DegQ


Theoretical massNumber of molelcules
Total (without water)22,2224
Polymers22,2224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-66 kcal/mol
Surface area9730 Å2
MethodPISA
2
E: Degradation enzyme regulation protein DegQ
F: Degradation enzyme regulation protein DegQ
G: Degradation enzyme regulation protein DegQ
H: Degradation enzyme regulation protein DegQ


Theoretical massNumber of molelcules
Total (without water)22,2224
Polymers22,2224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-67 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.548, 52.271, 53.098
Angle α, β, γ (deg.)87.443, 89.567, 89.936
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
Degradation enzyme regulation protein DegQ / Regulatory factor SacQ


Mass: 5555.444 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: Miyagino / Gene: degQ, amyB, sacQ, BSU31720 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99039
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.1 Å3/Da / Density % sol: 41.55 % / Description: plate-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15%(v/v) polyethylene glycol 3350, 5 mM magnesium chloride, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 15256 / % possible obs: 95.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.032 / Rrim(I) all: 0.059 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.349 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 764 / Rpim(I) all: 0.126 / Rrim(I) all: 0.235 / % possible all: 81.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
STARANISOdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.3→38.1 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.031 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.267
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2542 780 5.113 %
Rwork0.2196 14476 -
all0.221 --
obs-15256 95.344 %
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: 43.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.238 Å2-1.156 Å2-0.815 Å2
2---0.471 Å2-0.558 Å2
3---0.641 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 0 86 2829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122753
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162846
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9073660
X-RAY DIFFRACTIONr_angle_other_deg0.4931.8426591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.865316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.479516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81410654
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.05910142
X-RAY DIFFRACTIONr_chiral_restr0.0640.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_nbd_refined0.2330.2669
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22568
X-RAY DIFFRACTIONr_nbtor_refined0.180.21330
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.21679
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0770.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.28
X-RAY DIFFRACTIONr_nbd_other0.210.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2310.25
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0190.21
X-RAY DIFFRACTIONr_mcbond_it3.6214.031288
X-RAY DIFFRACTIONr_mcbond_other3.624.031288
X-RAY DIFFRACTIONr_mcangle_it6.0297.1531596
X-RAY DIFFRACTIONr_mcangle_other6.0287.1561597
X-RAY DIFFRACTIONr_scbond_it4.0874.8541465
X-RAY DIFFRACTIONr_scbond_other4.0854.8571466
X-RAY DIFFRACTIONr_scangle_it6.9378.6232064
X-RAY DIFFRACTIONr_scangle_other6.9358.6252065
X-RAY DIFFRACTIONr_lrange_it10.64140.1823190
X-RAY DIFFRACTIONr_lrange_other10.63940.1963190
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
2.3-2.360.321510.2419140.24511690.9460.96782.54920.212
2.36-2.4240.249540.24210080.24211630.9680.96891.31560.214
2.424-2.4940.338240.23610140.23810980.9660.9794.53550.206
2.494-2.570.186510.2129820.21110940.980.97594.42410.187
2.57-2.6540.315600.2159220.22110320.9530.97495.1550.199
2.654-2.7470.229400.2069770.20710490.9660.97796.94950.189
2.747-2.850.3640.2048870.219740.9480.97597.63860.192
2.85-2.9660.276420.2178860.229520.9510.97397.4790.206
2.966-3.0970.201350.2128680.2119210.9730.97798.04560.212
3.097-3.2470.216430.2367870.2358420.9720.97598.57480.235
3.247-3.4210.304360.2317880.2348360.940.97898.56460.234
3.421-3.6270.244420.2277310.2287850.970.97998.47130.231
3.627-3.8750.226520.1886640.1917270.9810.98198.48690.199
3.875-4.1810.205510.1736400.1756990.9820.98398.85550.191
4.181-4.5750.308270.1715700.1776110.9460.98297.70870.198
4.575-5.1060.246350.1825120.1865710.9690.98295.79680.216
5.106-5.8780.283270.284650.285120.9710.96896.09380.323
5.878-7.1570.328190.3363850.3364270.9680.95994.61360.377
7.157-9.9470.248120.312960.3083320.9810.9892.77110.391
9.947-38.10.284150.3041800.3032020.9760.96996.53470.496

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