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- PDB-7ewe: Mycobacterium tuberculosis HigA2 (Form III) -

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Basic information

Entry
Database: PDB / ID: 7ewe
TitleMycobacterium tuberculosis HigA2 (Form III)
ComponentsPutative antitoxin HigA2
KeywordsDNA BINDING PROTEIN / Antitoxin / HigA2
Function / homologyHelix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Putative antitoxin HigA2
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å
AuthorsKim, H.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1G1A1100821 Korea, Republic Of
CitationJournal: Iucrj / Year: 2021
Title: Chasing the structural diversity of the transcription regulator Mycobacterium tuberculosis HigA2.
Authors: Richardson, W. / Kang, G.W. / Lee, H.J. / Kwon, K.M. / Kim, S. / Kim, H.J.
History
DepositionMay 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative antitoxin HigA2
B: Putative antitoxin HigA2
C: Putative antitoxin HigA2
D: Putative antitoxin HigA2
E: Putative antitoxin HigA2


Theoretical massNumber of molelcules
Total (without water)56,5505
Polymers56,5505
Non-polymers00
Water00
1
A: Putative antitoxin HigA2
B: Putative antitoxin HigA2


Theoretical massNumber of molelcules
Total (without water)22,6202
Polymers22,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-15 kcal/mol
Surface area7870 Å2
MethodPISA
2
C: Putative antitoxin HigA2
D: Putative antitoxin HigA2


Theoretical massNumber of molelcules
Total (without water)22,6202
Polymers22,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-13 kcal/mol
Surface area8000 Å2
MethodPISA
3
E: Putative antitoxin HigA2

E: Putative antitoxin HigA2


Theoretical massNumber of molelcules
Total (without water)22,6202
Polymers22,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area2170 Å2
ΔGint-8 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.890, 86.890, 153.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Putative antitoxin HigA2


Mass: 11309.927 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: higA2, Rv2021c, RVBD_2021c, LH57_11010, P425_02092 / Production host: Escherichia coli (E. coli) / References: UniProt: O53467

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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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) PEG 4000, 0.2M ammonium sulfate, 0.1M sodium acetate trihydrate pH4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.4→76.96 Å / Num. obs: 9603 / % possible obs: 97.8 % / Redundancy: 4.9 % / CC1/2: 0.997 / Net I/σ(I): 7.9
Reflection shellResolution: 3.41→3.68 Å / Num. unique obs: 1930 / CC1/2: 0.507

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ewc

7ewc


Resolution: 3.41→75.36 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 39.511 / SU ML: 0.582 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.523 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 450 4.7 %RANDOM
Rwork0.2023 ---
obs0.2063 9126 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 353.87 Å2 / Biso mean: 126.493 Å2 / Biso min: 72.37 Å2
Baniso -1Baniso -2Baniso -3
1--4.14 Å2-2.07 Å20 Å2
2---4.14 Å20 Å2
3---13.43 Å2
Refinement stepCycle: final / Resolution: 3.41→75.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 0 0 2695
Num. residues----352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132710
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172653
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.6343653
X-RAY DIFFRACTIONr_angle_other_deg1.2131.5776067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7465347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07419.639166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.29415485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0871538
X-RAY DIFFRACTIONr_chiral_restr0.0590.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023077
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02617
LS refinement shellResolution: 3.41→3.499 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 29 -
Rwork0.404 656 -
all-685 -
obs--98.85 %

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