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- PDB-6cf1: Proteus vulgaris HigA antitoxin structure -

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Basic information

Entry
Database: PDB / ID: 6cf1
TitleProteus vulgaris HigA antitoxin structure
ComponentsAntitoxin HigA
KeywordsANTITOXIN / Helix-turn-helix motif / transcriptional regulator / toxin-antitoxin
Function / homology
Function and homology information


toxin sequestering activity / transcription cis-regulatory region binding / protein heterodimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Toxin-antitoxin system, antidote protein, HigA / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / 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
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchureck, M.A. / Hoffer, E.D. / Ei Cho, S. / Dunham, C.M.
CitationJournal: Mol.Microbiol. / Year: 2019
Title: Structural basis of transcriptional regulation by the HigA antitoxin.
Authors: Schureck, M.A. / Meisner, J. / Hoffer, E.D. / Wang, D. / Onuoha, N. / Ei Cho, S. / Lollar 3rd, P. / Dunham, C.M.
History
DepositionFeb 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Sep 18, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitoxin HigA
B: Antitoxin HigA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4017
Polymers30,2062
Non-polymers1955
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-22 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.610, 40.700, 45.320
Angle α, β, γ (deg.)90.00, 105.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

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Components

#1: Protein Antitoxin HigA / Antidote protein / Host inhibition of growth protein A


Mass: 15102.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: higA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q7A224
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.54 Å3/Da / Density % sol: 20.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M NaSCN and 20% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2013
RadiationMonochromator: KOHZU DIAMOND MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→43.672 Å / Num. obs: 14531 / % possible obs: 98.9 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rrim(I) all: 0.123 / Net I/σ(I): 11.38
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.62 / Num. unique obs: 2046 / CC1/2: 0.838 / Rrim(I) all: 0.718 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSVERSION May 1, 2016data reduction
XSCALEVERSION May 1, 2016data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MCT

4mct


Resolution: 1.9→43.672 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.56
RfactorNum. reflection% reflection
Rfree0.2181 1454 10.01 %
Rwork0.1804 --
obs0.1843 14528 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→43.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 5 146 1578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141461
X-RAY DIFFRACTIONf_angle_d1.3481982
X-RAY DIFFRACTIONf_dihedral_angle_d14.798543
X-RAY DIFFRACTIONf_chiral_restr0.099228
X-RAY DIFFRACTIONf_plane_restr0.008260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.28731450.27861298X-RAY DIFFRACTION99
1.9679-2.04670.30991420.23611284X-RAY DIFFRACTION99
2.0467-2.13980.2321440.19541295X-RAY DIFFRACTION99
2.1398-2.25260.2421480.18571331X-RAY DIFFRACTION100
2.2526-2.39370.22211430.16611282X-RAY DIFFRACTION99
2.3937-2.57850.20551420.16761277X-RAY DIFFRACTION98
2.5785-2.8380.22451480.16351332X-RAY DIFFRACTION100
2.838-3.24850.21261440.16821304X-RAY DIFFRACTION99
3.2485-4.09230.1951490.16091332X-RAY DIFFRACTION99
4.0923-43.68330.20281490.18911339X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1211-0.23751.07542.4981-3.5175.44960.0921-0.1549-0.14280.01460.04670.52150.0143-0.3114-0.12380.20720.01460.0420.26740.03190.2966-22.4217-9.97975.2592
28.7029-1.4141-1.45744.33461.20486.23590.0545-0.6201-0.46190.42590.0072-0.20130.35280.42810.08140.2125-0.0211-0.00530.25370.05870.2207-8.3918-18.35118.0585
34.4627-2.91470.39643.8545-3.23985.104-0.2247-0.22890.31770.31420.0719-0.2103-0.8999-0.07170.0420.2696-0.0252-0.02450.2413-0.04510.2367-9.6757-6.86146.3141
41.6546-2.0162-0.02064.7879-0.31630.405-0.04480.03420.02510.0520.0660.1012-0.08570.1042-0.00490.2273-0.01610.01570.20920.00360.1745-16.4911-7.6817-4.1704
53.64470.816-2.55486.542-3.53923.41850.0416-0.0621-0.10490.19360.04670.1264-0.5721-0.31770.09730.19690.0211-0.00110.24080.0010.2964-25.094414.5583-11.977
66.6135-4.40553.88294.740.04416.17070.38850.5555-0.2361-1.2813-0.4245-0.12390.83470.3066-0.00730.43750.02740.06910.3388-0.02850.2946-11.88417.8106-23.4153
74.1335-2.6449-2.53553.53580.2192.6354-0.0713-0.06160.25290.0027-0.183-0.2171-0.62110.18050.17840.286-0.0025-0.04040.24440.03580.2516-14.882520.2866-18.0507
88.9975-5.2374-2.52814.70544.9748.1265-0.2732-0.3774-0.4529-0.0010.0877-0.50760.19320.43150.10190.2407-0.02360.05770.23110.0460.283-8.770315.2233-12.8552
92.8701-1.1144-0.47673.5966-0.43543.00440.2118-0.0844-0.0528-0.1319-0.0789-0.19730.0730.1047-0.05260.1682-0.0060.0380.1417-0.00660.1599-16.34658.6722-12.6692
104.4997-5.48552.29538.2482-0.88123.50720.29370.3754-0.0328-0.4-0.3008-0.27170.21650.1465-0.06440.1958-0.02260.03110.18140.01220.2036-12.9553-1.9971-14.2438
114.39134.0511-2.38634.0688-2.30944.21360.17050.3949-0.1520.0357-0.1571-0.3783-0.04020.14210.06380.26830.0394-0.01940.33950.00990.3627-7.6118-20.5331-5.2491
125.5095-5.0586-4.8858.70673.27184.740.286-0.6620.3840.42221.1481-1.0671-0.14020.7246-0.20290.4696-0.006-0.08070.5821-0.02660.5293-6.0074-34.4295-5.7561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 49 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 79 )
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 94 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 20 )
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 31 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 42 )
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 63 )
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 79 )
11X-RAY DIFFRACTION11chain 'B' and (resid 80 through 94 )
12X-RAY DIFFRACTION12chain 'B' and (resid 95 through 99 )

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