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

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Basic information

Entry
Database: PDB / ID: 9vvt
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 / SAD / Resolution: 2.5 Å
AuthorsCho, H.J. / 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


Theoretical massNumber of molelcules
Total (without water)70,4292
Polymers70,4292
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-41 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.500, 92.079, 126.190
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: 35214.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium sp. DSM 3803 (bacteria) / Gene: cutR / Production host: Escherichia coli (E. coli) / References: UniProt: D5G1X9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion / pH: 7.5 / Details: 5% PEG 8000, 0.1 M sodium acetate, 4% glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26309 / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.113 / Χ2: 2.465 / Net I/σ(I): 11.8 / Num. measured all: 375109
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.5-2.5914.50.48725811.0491100
2.59-2.6914.60.3825761.1261100
2.69-2.8214.70.30125981.2541100
2.82-2.9614.60.23325971.4571100
2.96-3.1514.60.17825951.871100
3.15-3.3914.50.1426092.2911100
3.39-3.7314.30.10826513.0351100
3.73-4.2714.10.09826143.8691100
4.27-5.3813.80.08626734.1491100
5.38-50130.07528154.739199.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data scaling
DENZOdata reduction
SOLVEphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.5→40.26 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 20.628 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.645 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26804 1252 5.1 %RANDOM
Rwork0.212 ---
obs0.21479 23187 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.494 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.5→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4881 0 0 44 4925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224983
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.976770
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6895649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20721.97198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87715822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6941555
X-RAY DIFFRACTIONr_chiral_restr0.0740.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023749
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.22160
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23410
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5331.53334
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79325194
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.08931821
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7484.51575
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 70 -
Rwork0.229 1489 -
obs--100 %

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