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- PDB-7r22: Crystal structure of protein Mab3862 from Mycobacterium abscessus -

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Basic information

Entry
Database: PDB / ID: 7r22
TitleCrystal structure of protein Mab3862 from Mycobacterium abscessus
ComponentsArsR family transcriptional regulator
KeywordsANTITOXIN / toxin / Mycobacterium abscessus.putative ArsR family transcriptional regulator
Function / homologyHelix-turn-helix domain / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily / ArsR family transcriptional regulator
Function and homology information
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å
AuthorsKim, S.Y. / Eun, H.J. / Lee, J.Y. / Lee, B.J. / Blundell, T.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: To Be Published
Title: Structure of putative ArsR family regulator antitoxin from Mycobacterium abscessus (MAB_3862)
Authors: Kim, S.Y.
History
DepositionFeb 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ArsR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)16,7971
Polymers16,7971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7630 Å2
Unit cell
Length a, b, c (Å)106.886, 106.886, 106.886
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4

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Components

#1: Protein ArsR family transcriptional regulator


Mass: 16797.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: D2E76_02065 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A418LEB3
Has ligand of interestY
Has protein modificationY

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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: 4.47 Å3/Da / Density % sol: 72.46 %
Crystal growTemperature: 298 K / Method: batch mode / Details: Sodium acetate pH 5.0 50mM Ammonium sulphate 2.0M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.73→75.88 Å / Num. obs: 5863 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.125 / Net I/σ(I): 26.8
Reflection shellResolution: 2.73→2.78 Å / Num. unique obs: 296 / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoPROCdata reduction
autoPROCdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.73→47.8 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3473 --
Rwork0.2992 --
obs0.32 1083 75.52 %
Refinement stepCycle: LAST / Resolution: 2.73→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 0 0 780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127787
X-RAY DIFFRACTIONf_angle_d2.04461056
X-RAY DIFFRACTIONf_chiral_restr0.0666120
X-RAY DIFFRACTIONf_plane_restr0.007139
X-RAY DIFFRACTIONf_dihedral_angle_d27.0561296

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