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- PDB-2ict: Crystal structure of the bacterial antitoxin HigA from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 2ict
TitleCrystal structure of the bacterial antitoxin HigA from Escherichia coli at pH 8.5. Northeast Structural Genomics TARGET ER390.
Componentsantitoxin higa
KeywordsDNA BINDING PROTEIN / helix-turn-helix / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Toxin-antitoxin system, antidote protein, HigA / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized HTH-type transcriptional regulator YddM / Uncharacterized HTH-type transcriptional regulator YddM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsArbing, M.A. / Abashidze, M. / Hurley, J.M. / Zhao, L. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. ...Arbing, M.A. / Abashidze, M. / Hurley, J.M. / Zhao, L. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Inouye, M. / Woychik, N.A. / Montelione, G.T. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Structure / Year: 2010
Title: Crystal Structures of Phd-Doc, HigA, and YeeU Establish Multiple Evolutionary Links between Microbial Growth-Regulating Toxin-Antitoxin Systems.
Authors: Arbing, M.A. / Handelman, S.K. / Kuzin, A.P. / Verdon, G. / Wang, C. / Su, M. / Rothenbacher, F.P. / Abashidze, M. / Liu, M. / Hurley, J.M. / Xiao, R. / Acton, T. / Inouye, M. / Montelione, ...Authors: Arbing, M.A. / Handelman, S.K. / Kuzin, A.P. / Verdon, G. / Wang, C. / Su, M. / Rothenbacher, F.P. / Abashidze, M. / Liu, M. / Hurley, J.M. / Xiao, R. / Acton, T. / Inouye, M. / Montelione, G.T. / Woychik, N.A. / Hunt, J.F.
History
DepositionSep 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antitoxin higa


Theoretical massNumber of molelcules
Total (without water)10,6481
Polymers10,6481
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: antitoxin higa

A: antitoxin higa


Theoretical massNumber of molelcules
Total (without water)21,2952
Polymers21,2952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3240 Å2
ΔGint-24 kcal/mol
Surface area10610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.535, 26.364, 39.485
Angle α, β, γ (deg.)90.00, 91.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein antitoxin higa / Putative HTH-type transcriptional regulator yddM


Mass: 10647.538 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: higa / Plasmid: pET28-HigA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ MAGIC / References: UniProt: P67699, UniProt: P67700*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: under oil. / pH: 8.5
Details: 5 mM MgSO4, 50 mM Tris pH 8.5, 35% 1,6-Hexanediol, Under oil., temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97941 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionRedundancy: 5.7 % / Av σ(I) over netI: 6.9 / Number: 67242 / Rmerge(I) obs: 0.237 / Χ2: 1.44 / D res high: 1.63 Å / D res low: 30 Å / Num. obs: 11696 / % possible obs: 98.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.423010010.1721.8166.2
3.514.4299.810.1391.3836.5
3.073.5110010.1571.6226.5
2.793.0799.210.191.556.5
2.592.7999.310.2391.9286.5
2.432.5999.210.2651.7396.5
2.312.4399.310.2881.6166.4
2.212.3199.710.3491.6396.3
2.132.2198.510.3831.5436.3
2.052.1398.410.4281.3316.1
1.992.0599.710.51.4596
1.931.9997.310.5741.3765.9
1.881.9399.810.6731.2015.6
1.841.8897.310.7131.1565.6
1.791.849910.8251.1675.3
1.761.7995.510.8021.1095
1.721.7698.711.0614.8
1.691.7295.511.134.6
1.661.6997.111.1564.2
1.631.6695.410.9883.8
ReflectionResolution: 1.63→30 Å / Num. obs: 11696 / % possible obs: 98.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.237 / Χ2: 1.442 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.63-1.663.85440.988195.4
1.66-1.694.25781.156197.1
1.69-1.724.65461.13195.5
1.72-1.764.85901.061198.7
1.76-1.7955471.109195.50.802
1.79-1.845.35801.1671990.825
1.84-1.885.66101.156197.30.713
1.88-1.935.65501.201199.80.673
1.93-1.995.95821.376197.30.574
1.99-2.0566021.459199.70.5
2.05-2.136.15701.331198.40.428
2.13-2.216.35891.543198.50.383
2.21-2.316.35801.639199.70.349
2.31-2.436.45971.616199.30.288
2.43-2.596.55881.739199.20.265
2.59-2.796.55961.928199.30.239
2.79-3.076.55911.55199.20.19
3.07-3.516.55941.62211000.157
3.51-4.426.56301.383199.80.139
4.42-306.26321.81611000.172

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Phasing

Phasing MRRfactor: 48.7 / Cor.coef. Fo:Fc: 38.62
Highest resolutionLowest resolution
Rotation4 Å15 Å
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMO1.2phasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→30 Å / FOM work R set: 0.904 / σ(F): 1360
RfactorNum. reflection% reflection
Rfree0.201 506 4.2 %
Rwork0.198 --
obs-9805 82.3 %
Solvent computationBsol: 36.819 Å2
Displacement parametersBiso mean: 22.007 Å2
Baniso -1Baniso -2Baniso -3
1-3.321 Å20 Å2-2.39 Å2
2---3.601 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.63→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 0 0 96 823
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.63-1.690.34230.247580603
1.69-1.760.199390.247676715
1.76-1.840.222320.22774806
1.84-1.930.203480.201873921
1.93-2.050.218490.2029781027
2.05-2.210.196310.1910451076
2.21-2.430.238730.19310251098
2.43-2.790.182640.18910771141
2.79-3.510.193640.19311001164
3.51-400.188830.19411711254
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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