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- PDB-7ewd: Mycobacterium tuberculosis HigA2 (Form II) -

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Basic information

Entry
Database: PDB / ID: 7ewd
TitleMycobacterium tuberculosis HigA2 (Form II)
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: 3.2 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


Theoretical massNumber of molelcules
Total (without water)45,2404
Polymers45,2404
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 area2440 Å2
ΔGint-11 kcal/mol
Surface area8170 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 area2340 Å2
ΔGint-14 kcal/mol
Surface area7710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.621, 67.621, 190.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Putative antitoxin HigA2


Mass: 11309.927 Da / Num. of mol.: 4
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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% (w/v) PEK 8000, 8% (v/v) ethylene glycol, 0.1M HEPES pH 7.5

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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: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 7877 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.979 / Rmerge(I) obs: 0.105 / Net I/σ(I): 24.7
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 382 / CC1/2: 0.892

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ewc

7ewc


Resolution: 3.2→38.96 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 18.131 / SU ML: 0.316 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 383 4.9 %RANDOM
Rwork0.2121 ---
obs0.215 7494 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 260.31 Å2 / Biso mean: 99.6 Å2 / Biso min: 41.33 Å2
Baniso -1Baniso -2Baniso -3
1-14.24 Å20 Å20 Å2
2--14.24 Å20 Å2
3----28.49 Å2
Refinement stepCycle: final / Resolution: 3.2→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 0 0 2219
Num. residues----289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132249
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172203
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.6373029
X-RAY DIFFRACTIONr_angle_other_deg1.3011.5795036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6295287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.3819.441143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.92115408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5611534
X-RAY DIFFRACTIONr_chiral_restr0.0620.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022558
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02516
LS refinement shellResolution: 3.2→3.28 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.264 28 -
Rwork0.215 536 -
obs--99.47 %

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