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- PDB-9vvu: Crystal structure of the LysR-type transcriptional regulator CutR... -

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Basic information

Entry
Database: PDB / ID: 9vvu
TitleCrystal structure of the LysR-type transcriptional regulator CutR from mycobacterium sp. strain JC1
ComponentsLysR family transcriptional regulator
KeywordsTRANSCRIPTION / LysR family transcriptional regulator
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
LysR family transcriptional regulator
Similarity search - Component
Biological speciesMycobacterium sp. DSM 3803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCho, H.J. / Lee, K.Y. / Kang, B.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2025
Title: Symmetric Dimeric Structure and Ligand Recognition of CutR, a LysR-Type Transcriptional Regulator from Mycobacterium sp. Strain JC1.
Authors: Cho, H.J. / Lee, K.Y. / Lee, H.S. / Kang, B.S.
History
DepositionJul 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LysR family transcriptional regulator
B: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6515
Polymers68,4352
Non-polymers2163
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-33 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.933, 81.809, 101.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LysR family transcriptional regulator


Mass: 34217.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium sp. DSM 3803 (bacteria) / Strain: DSM 3893 / JC1 / Gene: cutR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D5G1X9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5% PEG8000, 0.1 M Sodium Acetate, 4% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 52582 / % possible obs: 96.5 % / Redundancy: 6.4 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Χ2: 1.976 / Net I/σ(I): 16 / Num. measured all: 337472
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.8-1.833.80.56920360.7530.9270.3190.6561.49976.4
1.83-1.864.10.50221760.810.9460.2680.5731.54181.3
1.86-1.94.40.4323600.8790.9670.2210.4861.59287.8
1.9-1.944.70.33925470.9050.9750.1670.381.66594.3
1.94-1.985.40.29526350.9360.9830.1380.3281.76298.3
1.98-2.036.50.25726960.9630.9910.1090.281.91399.6
2.03-2.086.90.21726840.9740.9930.0890.2351.99899.9
2.08-2.136.90.18726760.980.9950.0760.2022.01899.9
2.13-2.26.90.15727300.9870.9970.0640.172.075100
2.2-2.2770.13226920.9880.9970.0540.1432.10899.9
2.27-2.357.10.11727250.9920.9980.0470.1272.054100
2.35-2.447.10.10326740.9930.9980.0420.1122.117100
2.44-2.557.20.08827310.9940.9990.0350.0952.118100
2.55-2.697.20.07927220.9960.9990.0320.0852.121100
2.69-2.867.20.06827150.9970.9990.0270.0732.15399.9
2.86-3.087.20.0627500.9970.9990.0240.0652.175100
3.08-3.397.10.05127400.9980.9990.020.0552.11699.9
3.39-3.887.10.04327770.99810.0170.0461.95199.8
3.88-4.886.80.03827700.99810.0160.0411.70499.2
4.88-506.10.03827460.9980.9990.0170.0421.83792.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
DENZOdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→36.62 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2334 1949 3.83 %
Rwork0.1905 --
obs0.1921 50949 93.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4791 0 14 398 5203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054893
X-RAY DIFFRACTIONf_angle_d0.7366642
X-RAY DIFFRACTIONf_dihedral_angle_d21.819701
X-RAY DIFFRACTIONf_chiral_restr0.05783
X-RAY DIFFRACTIONf_plane_restr0.007869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.341020.25572505X-RAY DIFFRACTION68
1.84-1.890.30541130.23832830X-RAY DIFFRACTION76
1.89-1.950.3011280.22263210X-RAY DIFFRACTION87
1.95-2.010.26091380.2193444X-RAY DIFFRACTION94
2.01-2.090.26841430.21223598X-RAY DIFFRACTION97
2.09-2.170.2461460.20633636X-RAY DIFFRACTION98
2.17-2.270.2471470.19923652X-RAY DIFFRACTION98
2.27-2.390.23841440.19323638X-RAY DIFFRACTION98
2.39-2.540.26731460.19423708X-RAY DIFFRACTION99
2.54-2.730.23321480.20623728X-RAY DIFFRACTION99
2.73-3.010.25111460.21013728X-RAY DIFFRACTION99
3.01-3.440.2661490.18853748X-RAY DIFFRACTION100
3.44-4.340.1841500.16243812X-RAY DIFFRACTION100
4.34-36.620.19311490.17193763X-RAY DIFFRACTION95

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