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- PDB-8zde: Crystal structure of HsmR with DNA bound -

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Basic information

Entry
Database: PDB / ID: 8zde
TitleCrystal structure of HsmR with DNA bound
Components
  • DNA (5'-D(*AP*AP*TP*GP*GP*TP*TP*TP*GP*CP*AP*TP*AP*CP*AP*AP*AP*CP*TP*AP*AP*T)-3')
  • DNA (5'-D(*AP*TP*TP*AP*GP*TP*TP*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*CP*CP*AP*TP*T)-3')
  • MarR-family transcriptional regulator
KeywordsTRANSCRIPTION / MarR
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / MarR-family transcriptional regulator
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsPark, S.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of C. difficile HsmR with DNA bound
Authors: Park, S.Y. / Rho, S.H.
History
DepositionMay 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MarR-family transcriptional regulator
B: MarR-family transcriptional regulator
C: MarR-family transcriptional regulator
D: MarR-family transcriptional regulator
E: MarR-family transcriptional regulator
F: MarR-family transcriptional regulator
G: DNA (5'-D(*AP*TP*TP*AP*GP*TP*TP*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*CP*CP*AP*TP*T)-3')
H: DNA (5'-D(*AP*AP*TP*GP*GP*TP*TP*TP*GP*CP*AP*TP*AP*CP*AP*AP*AP*CP*TP*AP*AP*T)-3')
I: DNA (5'-D(*AP*TP*TP*AP*GP*TP*TP*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*CP*CP*AP*TP*T)-3')
J: DNA (5'-D(*AP*AP*TP*GP*GP*TP*TP*TP*GP*CP*AP*TP*AP*CP*AP*AP*AP*CP*TP*AP*AP*T)-3')
K: DNA (5'-D(*AP*TP*TP*AP*GP*TP*TP*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*CP*CP*AP*TP*T)-3')
L: DNA (5'-D(*AP*AP*TP*GP*GP*TP*TP*TP*GP*CP*AP*TP*AP*CP*AP*AP*AP*CP*TP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,73014
Polymers156,65212
Non-polymers782
Water43224
1
A: MarR-family transcriptional regulator
B: MarR-family transcriptional regulator
G: DNA (5'-D(*AP*TP*TP*AP*GP*TP*TP*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*CP*CP*AP*TP*T)-3')
H: DNA (5'-D(*AP*AP*TP*GP*GP*TP*TP*TP*GP*CP*AP*TP*AP*CP*AP*AP*AP*CP*TP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2565
Polymers52,2174
Non-polymers391
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-84 kcal/mol
Surface area19080 Å2
MethodPISA
2
C: MarR-family transcriptional regulator
D: MarR-family transcriptional regulator
I: DNA (5'-D(*AP*TP*TP*AP*GP*TP*TP*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*CP*CP*AP*TP*T)-3')
J: DNA (5'-D(*AP*AP*TP*GP*GP*TP*TP*TP*GP*CP*AP*TP*AP*CP*AP*AP*AP*CP*TP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2565
Polymers52,2174
Non-polymers391
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11870 Å2
ΔGint-87 kcal/mol
Surface area18240 Å2
MethodPISA
3
E: MarR-family transcriptional regulator
F: MarR-family transcriptional regulator
K: DNA (5'-D(*AP*TP*TP*AP*GP*TP*TP*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*CP*CP*AP*TP*T)-3')
L: DNA (5'-D(*AP*AP*TP*GP*GP*TP*TP*TP*GP*CP*AP*TP*AP*CP*AP*AP*AP*CP*TP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)52,2174
Polymers52,2174
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-79 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)262.113, 55.705, 117.525
Angle α, β, γ (deg.)90.00, 101.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
MarR-family transcriptional regulator


Mass: 19359.271 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: CDR20291_0782 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9R0BIW1
#2: DNA chain DNA (5'-D(*AP*TP*TP*AP*GP*TP*TP*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*CP*CP*AP*TP*T)-3')


Mass: 6740.388 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: (DA)(DT)(DT)(DA)(DG)(DT)(DT)(DT)(DG)(DT)(DA)(DT)(DG)(DC)(DA)(DA)(DA)(DC)(DC)(DA) (DT)(DT)
Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain DNA (5'-D(*AP*AP*TP*GP*GP*TP*TP*TP*GP*CP*AP*TP*AP*CP*AP*AP*AP*CP*TP*AP*AP*T)-3')


Mass: 6758.416 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: (DA)(DA)(DT)(DG)(DG)(DT)(DT)(DT)(DG)(DC)(DA)(DT)(DA)(DC)(DA)(DA)(DA)(DC)(DT)(DA) (DA)(DT)
Source: (synth.) Clostridioides difficile (bacteria)
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M KCl, 35% PEP (5/4 PO/OH) and 50 mM HEPES (pH 7.5)

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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: 0.97179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97179 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 37178 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rrim(I) all: 0.133 / Net I/σ(I): 18.9
Reflection shellResolution: 2.9→2.95 Å / Num. unique obs: 1850 / CC1/2: 0.888 / Rrim(I) all: 1.093

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 22.096 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27599 1857 5 %RANDOM
Rwork0.21247 ---
obs0.21573 35124 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å27.02 Å2
2--2.34 Å2-0 Å2
3----5.98 Å2
Refinement stepCycle: 1 / Resolution: 2.91→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6810 2688 2 24 9524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0179909
X-RAY DIFFRACTIONr_bond_other_d0.0020.028315
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.70113870
X-RAY DIFFRACTIONr_angle_other_deg1.239319290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5835829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.85125.693332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.428151427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8061525
X-RAY DIFFRACTIONr_chiral_restr0.0910.21456
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029186
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022137
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.04210.0693334
X-RAY DIFFRACTIONr_mcbond_other6.03210.0693333
X-RAY DIFFRACTIONr_mcangle_it9.60415.0724157
X-RAY DIFFRACTIONr_mcangle_other9.60315.0734158
X-RAY DIFFRACTIONr_scbond_it6.3099.3226575
X-RAY DIFFRACTIONr_scbond_other6.3099.3226574
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.13113.8429714
X-RAY DIFFRACTIONr_long_range_B_refined13.84676.75612228
X-RAY DIFFRACTIONr_long_range_B_other13.84576.75412227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.91→2.981 Å
RfactorNum. reflection% reflection
Rfree0.38 108 -
Rwork-2494 -
obs--95.17 %

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