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- PDB-8xt8: Clostridioides difficile MarR (WP_003434724) with Hg-bound -

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Basic information

Entry
Database: PDB / ID: 8xt8
TitleClostridioides difficile MarR (WP_003434724) with Hg-bound
Components(MarR family transcriptional regulator) x 2
KeywordsTRANSCRIPTION / MarR
Function / homology: / :
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsPark, S. / Kwon, N.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00243435 Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Crystal structure of a Clostridioides difficile multiple antibiotic resistance regulator (MarR) CD0473 suggests a potential redox-regulated function.
Authors: Kwon, N. / Rho, S. / Ha, S.C. / Park, S.
History
DepositionJan 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: 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
C: MarR family transcriptional regulator
D: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,63112
Polymers69,0264
Non-polymers1,6058
Water1,820101
1
A: MarR family transcriptional regulator
B: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2606
Polymers35,4582
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-138 kcal/mol
Surface area15280 Å2
MethodPISA
2
C: MarR family transcriptional regulator
D: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3716
Polymers33,5692
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-141 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.602, 69.807, 94.659
Angle α, β, γ (deg.)90.00, 116.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MarR family transcriptional regulator


Mass: 16784.301 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: WP_003434724 / Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: mexR_2, SAMEA897059_03225 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9X9QLH1
#2: Protein MarR family transcriptional regulator


Mass: 18673.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WP_003434724 / Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: mexR_2, SAMEA897059_03225 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9X9QLH1
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 4.18 Å3/Da / Density % sol: 70.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 3.0 M NaCl, 0.1 M sodium acetate pH 4.5, and 10 mM DTT

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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: 1.00765 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00765 Å / Relative weight: 1
ReflectionResolution: 2.5→87.41 Å / Num. obs: 37635 / % possible obs: 98.5 % / Redundancy: 1.9 % / CC1/2: 0.994 / Net I/σ(I): 20.6
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 3763 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→87.41 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.291 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23843 1992 5 %RANDOM
Rwork0.19798 ---
obs0.20001 37635 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.855 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å20.99 Å2
2---2.61 Å2-0 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 2.5→87.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4593 0 8 101 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024655
X-RAY DIFFRACTIONr_bond_other_d0.0010.024607
X-RAY DIFFRACTIONr_angle_refined_deg2.011.9876244
X-RAY DIFFRACTIONr_angle_other_deg0.897310666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3395557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.84224.908218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84815964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7851529
X-RAY DIFFRACTIONr_chiral_restr0.1030.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02977
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_it5.2975.7772240
X-RAY DIFFRACTIONr_mcbond_other5.2865.7752239
X-RAY DIFFRACTIONr_mcangle_it7.7888.6452793
X-RAY DIFFRACTIONr_mcangle_other7.7888.6452794
X-RAY DIFFRACTIONr_scbond_it6.9046.4342415
X-RAY DIFFRACTIONr_scbond_other6.9036.4342416
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.4389.3163452
X-RAY DIFFRACTIONr_long_range_B_refined13.55745.5015546
X-RAY DIFFRACTIONr_long_range_B_other13.56645.4795534
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.561 Å
RfactorNum. reflection% reflection
Rfree0.376 147 -
Rwork0.318 2692 -
obs--97.23 %

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