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- PDB-7ewc: Mycobacterium tuberculosis HigA2 (Form I) -

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Basic information

Entry
Database: PDB / ID: 7ewc
TitleMycobacterium tuberculosis HigA2 (Form I)
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: 2.05 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
Water97354
1
A: Putative antitoxin HigA2
B: Putative antitoxin HigA2


Theoretical massNumber of molelcules
Total (without water)22,6202
Polymers22,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-14 kcal/mol
Surface area7590 Å2
MethodPISA
2
C: Putative antitoxin HigA2
D: Putative antitoxin HigA2


Theoretical massNumber of molelcules
Total (without water)22,6202
Polymers22,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-14 kcal/mol
Surface area7400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.610, 88.955, 114.961
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 1.73 Å3/Da / Density % sol: 28.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 11% (w/v) PEK 20000, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 20447 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.079 / Net I/σ(I): 29
Reflection shellResolution: 2.05→2.09 Å / Num. unique obs: 969 / CC1/2: 0.984

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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: 1Y7Y, 3B7H, 3KXA, 2A6C

1y7y

3b7h

3kxa

2a6c


Resolution: 2.05→35.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.201 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 988 4.8 %RANDOM
Rwork0.207 ---
obs0.209 19459 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.22 Å2 / Biso mean: 35.407 Å2 / Biso min: 12.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.46 Å2
Refinement stepCycle: final / Resolution: 2.05→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 0 54 2161
Biso mean---35.14 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132128
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172081
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.6342869
X-RAY DIFFRACTIONr_angle_other_deg1.4211.5774763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.18119.845129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.28415382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4541529
X-RAY DIFFRACTIONr_chiral_restr0.0850.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02477
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 84 -
Rwork0.226 1378 -
all-1462 -
obs--99.52 %

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