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- PDB-4z58: HipB-O3 20mer complex -

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Basic information

Entry
Database: PDB / ID: 4z58
TitleHipB-O3 20mer complex
Components
  • Antitoxin HipB
  • DNA (5'-D(*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*TP*AP*CP*GP*GP*GP*AP*TP*AP*A)-3')
KeywordsTranscription/DNA / HTH motif / Transcription repressor / HipA sequestering / Transcription-DNA complex
Function / homology
Function and homology information


toxin-antitoxin complex / regulation of growth / DNA-binding transcription repressor activity / core promoter sequence-specific DNA binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity
Similarity search - Function
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
DNA / DNA (> 10) / Antitoxin HipB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMin, J. / Brennan, R.G. / Schumacher, M.A.
CitationJournal: To be published
Title: Molecular mechanism on hipBA gene regulation.
Authors: Min, J. / Wang, A. / Brennan, R.G. / Schumacher, M.A.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitoxin HipB
B: DNA (5'-D(*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*TP*AP*CP*GP*GP*GP*AP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)14,1692
Polymers14,1692
Non-polymers00
Water1,71195
1
A: Antitoxin HipB
B: DNA (5'-D(*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*TP*AP*CP*GP*GP*GP*AP*TP*AP*A)-3')

A: Antitoxin HipB
B: DNA (5'-D(*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*TP*AP*CP*GP*GP*GP*AP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)28,3384
Polymers28,3384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
Buried area7050 Å2
ΔGint-52 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.941, 126.941, 126.941
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Antitoxin HipB


Mass: 8060.239 Da / Num. of mol.: 1 / Fragment: UNP residues 4-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hipB, b1508, JW1501 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS-T1 / References: UniProt: P23873
#2: DNA chain DNA (5'-D(*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*TP*AP*CP*GP*GP*GP*AP*TP*AP*A)-3') / Operator 3 of hiBA operon


Mass: 6108.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 6, 2013
RadiationMonochromator: Rigaku Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 12717 / % possible obs: 100 % / Redundancy: 22.3 % / Rmerge(I) obs: 0.081 / Χ2: 1.012 / Net I/av σ(I): 47.01 / Net I/σ(I): 11.6 / Num. measured all: 283883
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5420.90.8496150.7311100
2.54-2.5921.30.7846080.7631100
2.59-2.6421.50.7426220.7661100
2.64-2.6921.80.6596070.8041100
2.69-2.7521.90.5766220.8461100
2.75-2.8222.20.4456260.8891100
2.82-2.8922.40.3826180.9011100
2.89-2.9622.80.316210.9231100
2.96-3.0523.10.2616260.9711100
3.05-3.1523.20.2086281.0361100
3.15-3.2623.10.136161.11100
3.26-3.3923.20.1096331.1821100
3.39-3.5523.10.0836401.1721100
3.55-3.7323.10.0696281.1881100
3.73-3.9723.10.0586291.2111100
3.97-4.2722.90.0466481.1581100
4.27-4.722.70.0416481.2871100
4.7-5.3822.50.046581.055199.8
5.38-6.7822.10.0396760.9991100
6.78-5019.90.0317481.1181100

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.14data extraction
HKL-3000data scaling
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4Z52

4z52
PDB Unreleased entry


Resolution: 2.5→44.88 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8876 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.17 / Phase error: 17.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 1156 10.01 %
Rwork0.1921 10396 -
obs0.1937 11552 91.09 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.83 Å2 / Biso mean: 23.1269 Å2 / Biso min: 6.53 Å2
Refinement stepCycle: final / Resolution: 2.5→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms565 405 0 95 1065
Biso mean--0 28.12 -
Num. residues----91
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031026
X-RAY DIFFRACTIONf_angle_d0.8221470
X-RAY DIFFRACTIONf_chiral_restr0.04170
X-RAY DIFFRACTIONf_plane_restr0.002118
X-RAY DIFFRACTIONf_dihedral_angle_d22.865412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.61090.2591250.23451120124581
2.6109-2.74850.28621300.23371177130785
2.7485-2.92070.24331360.23041229136589
2.9207-3.14610.24231440.21881292143691
3.1461-3.46260.17641450.17861305145092
3.4626-3.96340.18141500.16611347149795
3.9634-4.99240.17621550.16431395155096
4.9924-44.88760.20661710.19091531170298

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