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- PDB-8za5: Crystal structure of HsmR -

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Basic information

Entry
Database: PDB / ID: 8za5
TitleCrystal structure of HsmR
ComponentsMarR-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
MarR-family transcriptional regulator
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
Authors: Park, S.Y. / Rho, S.H.
History
DepositionApr 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)38,7192
Polymers38,7192
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.875, 97.875, 56.855
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MarR-family transcriptional regulator


Mass: 19359.271 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MgCl2, 25 % (w/v) PEG 3350, and 0.1 M Bis-Tris pH 6.5

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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: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.2→84.76 Å / Num. obs: 16200 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 1 / Rrim(I) all: 0.114 / Net I/σ(I): 54.1
Reflection shellResolution: 2.2→2.24 Å / Mean I/σ(I) obs: 6.5 / Num. unique obs: 791 / CC1/2: 0.914 / Rrim(I) all: 1.353

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→84.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.712 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26421 802 5 %RANDOM
Rwork0.17846 ---
obs0.18259 15189 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.256 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 2.2→84.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 0 142 2384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192280
X-RAY DIFFRACTIONr_bond_other_d0.0020.022254
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.9613053
X-RAY DIFFRACTIONr_angle_other_deg1.03235199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.61125.545110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42915472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.291159
X-RAY DIFFRACTIONr_chiral_restr0.1090.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022529
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02516
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_it4.7124.9751100
X-RAY DIFFRACTIONr_mcbond_other4.6974.9731099
X-RAY DIFFRACTIONr_mcangle_it6.5137.4451372
X-RAY DIFFRACTIONr_mcangle_other6.5147.4481373
X-RAY DIFFRACTIONr_scbond_it6.295.9031180
X-RAY DIFFRACTIONr_scbond_other6.2875.9071181
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.818.5271681
X-RAY DIFFRACTIONr_long_range_B_refined12.32641.3422776
X-RAY DIFFRACTIONr_long_range_B_other12.2741.1062738
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 58 -
Rwork0.222 1054 -
obs--92.13 %

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