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- PDB-8xta: Clostridioides difficile MarR (WP_003434724) -

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Basic information

Entry
Database: PDB / ID: 8xta
TitleClostridioides difficile MarR (WP_003434724)
Components(MarR family transcriptional regulator) x 2
KeywordsTRANSCRIPTION / MarR
Function / homology:
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)69,0264
Polymers69,0264
Non-polymers00
Water2,234124
1
A: MarR family transcriptional regulator
B: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)35,4582
Polymers35,4582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-38 kcal/mol
Surface area15990 Å2
MethodPISA
2
C: MarR family transcriptional regulator
D: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)33,5692
Polymers33,5692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-37 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.483, 69.402, 95.007
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 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
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 4.21 Å3/Da / Density % sol: 70.82 %
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: 0.97933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.5→95.01 Å / Num. obs: 41080 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.995 / Net I/σ(I): 30.1
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 1988 / CC1/2: 0.781

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→95.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.821 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26019 2060 5 %RANDOM
Rwork0.20997 ---
obs0.21241 38935 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.444 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å2-0 Å20 Å2
2---1.7 Å20 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 2.5→95.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4602 0 0 124 4726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024664
X-RAY DIFFRACTIONr_bond_other_d0.0010.024620
X-RAY DIFFRACTIONr_angle_refined_deg2.0271.9876255
X-RAY DIFFRACTIONr_angle_other_deg0.917310697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2395558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34924.908218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.01615968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8741529
X-RAY DIFFRACTIONr_chiral_restr0.1060.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02978
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_it5.9125.6752244
X-RAY DIFFRACTIONr_mcbond_other5.9125.6742243
X-RAY DIFFRACTIONr_mcangle_it8.4868.4912798
X-RAY DIFFRACTIONr_mcangle_other8.4858.4922799
X-RAY DIFFRACTIONr_scbond_it6.96.2582418
X-RAY DIFFRACTIONr_scbond_other6.8996.2592419
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.4759.0733457
X-RAY DIFFRACTIONr_long_range_B_refined13.23444.2395539
X-RAY DIFFRACTIONr_long_range_B_other13.2444.2115520
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.503→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 155 -
Rwork0.338 2786 -
obs--98.03 %

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