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

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Basic information

Entry
Database: PDB / ID: 2icp
TitleCrystal structure of the bacterial antitoxin HigA from Escherichia coli at pH 4.0. Northeast Structural Genomics Consortium 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 / MOLECULAR REPLACEMENT / Resolution: 1.88 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: To be Published
Title: Crystal structure of the bacterial antitoxin HigA from Escherichia coli.
Authors: 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. / ...Authors: 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.
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 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antitoxin higa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6722
Polymers10,6481
Non-polymers241
Water1,33374
1


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

A: antitoxin higa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3444
Polymers21,2952
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3340 Å2
ΔGint-30 kcal/mol
Surface area9550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.127, 23.526, 41.593
Angle α, β, γ (deg.)90.00, 94.05, 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.85 Å3/Da / Density % sol: 33.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 200 mM MgCl2, 20% PEG 20K, 100 mM Na3Citrate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 17, 2005 / Details: Osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 2.5 % / Av σ(I) over netI: 18.4 / Number: 29182 / Rmerge(I) obs: 0.049 / Χ2: 1.05 / D res high: 1.88 Å / D res low: 60 Å / Num. obs: 11592 / % possible obs: 90.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.1609710.030.9972.8
4.055.198.410.0320.9032.8
3.544.0597.410.0370.9872.7
3.213.5497.310.0380.9952.7
2.983.2199.510.0481.0612.8
2.812.9895.510.0581.1182.7
2.672.8198.510.0521.0062.7
2.552.679410.0641.0562.7
2.452.5596.410.0690.9892.6
2.372.4597.710.081.1052.6
2.292.3790.910.0831.1532.6
2.232.2993.110.0891.1242.6
2.172.2394.910.0891.0482.5
2.122.179310.1031.1572.5
2.072.1288.710.1241.1012.4
2.032.078910.1371.0462.3
1.982.0387.710.151.0012.2
1.951.9883.810.1650.9862
1.911.9569.110.1891.0841.8
1.881.9155.110.1741.071.5
ReflectionResolution: 1.88→60 Å / Num. obs: 11592 / % possible obs: 90.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.049 / Χ2: 1.047 / Net I/σ(I): 18.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.88-1.911.50.1743411.07155.1
1.91-1.951.80.1894581.084169.1
1.95-1.9820.1655290.986183.8
1.98-2.032.20.155351.001187.7
2.03-2.072.30.1376051.046189
2.07-2.122.40.1245551.101188.7
2.12-2.172.50.1036111.157193
2.17-2.232.50.0895711.048194.9
2.23-2.292.60.0896081.124193.1
2.29-2.372.60.0835861.153190.9
2.37-2.452.60.085861.105197.7
2.45-2.552.60.0696430.989196.4
2.55-2.672.70.0646101.056194
2.67-2.812.70.0525991.006198.5
2.81-2.982.70.0586391.118195.5
2.98-3.212.80.0486321.061199.5
3.21-3.542.70.0386050.995197.3
3.54-4.052.70.0376260.987197.4
4.05-5.12.80.0326300.903198.4
5.1-602.80.036230.997197

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Phasing

Phasing MRRfactor: 42.7 / Cor.coef. Fo:Fc: 39.07
Highest resolutionLowest resolution
Rotation4 Å15 Å
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
CNSrefinement
SCALEPACKdata scaling
COMO1.2phasing
REFMACrefinement
PDB_EXTRACT2data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→40 Å / σ(F): 812
RfactorNum. reflection% reflection
Rfree0.225 1036 8.1 %
Rwork0.184 --
obs-10485 82 %
Solvent computationBsol: 71.638 Å2
Displacement parametersBiso mean: 23.711 Å2
Baniso -1Baniso -2Baniso -3
1--1.064 Å20 Å2-2.349 Å2
2--2.313 Å20 Å2
3----1.249 Å2
Refinement stepCycle: LAST / Resolution: 1.88→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms672 0 1 74 747
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.7831.5
X-RAY DIFFRACTIONc_scbond_it3.8752
X-RAY DIFFRACTIONc_mcangle_it2.7692
X-RAY DIFFRACTIONc_scangle_it6.2222.5
LS refinement shellResolution: 1.88→1.91 Å /
RfactorNum. reflection
Rfree0.351 21
Rwork0.267 -
obs-209
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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