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- PDB-8xu0: Clostridioides difficile MarR (WP_003434724) with salicylate -

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Basic information

Entry
Database: PDB / ID: 8xu0
TitleClostridioides difficile MarR (WP_003434724) with salicylate
Components(MarR) x 2
KeywordsTRANSCRIPTION / MarR
Function / homology2-HYDROXYBENZOIC ACID
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 12, 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

Downloads & links

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Assembly

Deposited unit
A: MarR
B: MarR
C: MarR
D: MarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5798
Polymers69,0264
Non-polymers5524
Water2,036113
1
A: MarR
B: MarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7344
Polymers35,4582
Non-polymers2762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-34 kcal/mol
Surface area15760 Å2
MethodPISA
2
C: MarR
D: MarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8454
Polymers33,5692
Non-polymers2762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-32 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.456, 69.172, 95.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MarR


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) / Production host: Escherichia coli (E. coli)
#2: Protein MarR


Mass: 16784.301 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 4.18 Å3/Da / Density % sol: 70.58 %
Crystal growTemperature: 289 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: 0.97935 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.29→95.12 Å / Num. obs: 52642 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.997 / Net I/σ(I): 33
Reflection shellResolution: 2.29→2.34 Å / Num. unique obs: 2564 / CC1/2: 0.693

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→95.12 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.259 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27236 2673 5.1 %RANDOM
Rwork0.2174 ---
obs0.2201 49824 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.087 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å2-0 Å20 Å2
2---1.04 Å20 Å2
3----1.52 Å2
Refinement stepCycle: 1 / Resolution: 2.29→95.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4610 0 40 113 4763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.024712
X-RAY DIFFRACTIONr_bond_other_d0.0010.024645
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.9956317
X-RAY DIFFRACTIONr_angle_other_deg0.923310750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0375559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59324.908218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.29115971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9691529
X-RAY DIFFRACTIONr_chiral_restr0.1180.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02995
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_it5.6285.5172248
X-RAY DIFFRACTIONr_mcbond_other5.6295.5162247
X-RAY DIFFRACTIONr_mcangle_it7.9138.2452803
X-RAY DIFFRACTIONr_mcangle_other7.9138.2462804
X-RAY DIFFRACTIONr_scbond_it6.7856.1582463
X-RAY DIFFRACTIONr_scbond_other6.7876.1572462
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.0888.9243514
X-RAY DIFFRACTIONr_long_range_B_refined12.69342.9235538
X-RAY DIFFRACTIONr_long_range_B_other12.69442.9175522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 216 -
Rwork0.298 3560 -
obs--98.46 %

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