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- PDB-4z5c: HipB-O3 21mer complex -

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Basic information

Entry
Database: PDB / ID: 4z5c
TitleHipB-O3 21mer complex
Components
  • Antitoxin HipB
  • DNA (5'-D(*TP*TP*TP*AP*TP*CP*CP*CP*GP*TP*AP*GP*AP*GP*CP*GP*GP*AP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*TP*AP*CP*GP*GP*GP*AP*TP*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 1.1Sep 27, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,6834
Polymers28,6834
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-56 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.027, 109.027, 58.796
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-110-

HOH

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Components

#1: Protein Antitoxin HipB


Mass: 8060.239 Da / Num. of mol.: 2 / 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 / Variant: MG1655 / 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*TP*AP*TP*CP*CP*CP*GP*TP*AP*GP*AP*GP*CP*GP*GP*AP*TP*AP*A)-3') / Operator 3 of hipBA operon / top strand


Mass: 6462.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*TP*AP*CP*GP*GP*GP*AP*TP*A)-3') / Operator 3 of hipBA operon / bottom strand


Mass: 6099.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: 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

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.02 M MgCl2, 0.05 M sodium cacodylate trihydrate, pH 6.0, 5% 2-propanol, 0.001 M spermine

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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 4, 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: 14130 / % possible obs: 99.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.08 / Χ2: 0.979 / Net I/av σ(I): 22.737 / Net I/σ(I): 11.8 / Num. measured all: 90409
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.544.30.6787030.79999.3
2.54-2.595.40.6697080.797100
2.59-2.646.10.6076940.829100
2.64-2.696.30.5827010.84100
2.69-2.756.50.5437060.856100
2.75-2.826.50.4337090.86899.9
2.82-2.896.60.3346880.898100
2.89-2.966.50.3026990.89699.7
2.96-3.056.70.2247140.977100
3.05-3.156.60.166960.95399.6
3.15-3.266.70.0947140.96599.9
3.26-3.396.70.0856881.03199.6
3.39-3.556.70.0737181.02599.3
3.55-3.736.70.0666981.06199.3
3.73-3.976.60.0617131.0899
3.97-4.276.80.0527061.10599
4.27-4.76.70.057091.26898.9
4.7-5.386.70.0487161.00797.8
5.38-6.786.70.0467081.03597.8
6.78-506.40.047421.12795.1

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4Z52

4z52
PDB Unreleased entry


Resolution: 2.5→49.91 Å / FOM work R set: 0.8423 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 1237 10 %
Rwork0.1921 11136 -
obs0.1959 12373 86.97 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.83 Å2 / Biso mean: 30.25 Å2 / Biso min: 12.96 Å2
Refinement stepCycle: final / Resolution: 2.5→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 833 0 95 2056
Biso mean---33.56 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092076
X-RAY DIFFRACTIONf_angle_d1.112977
X-RAY DIFFRACTIONf_chiral_restr0.07344
X-RAY DIFFRACTIONf_plane_restr0.005235
X-RAY DIFFRACTIONf_dihedral_angle_d25.527832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.60010.2519580.227555361139
2.6001-2.71840.27061140.25431122123680
2.7184-2.86170.29041440.26421262140690
2.8617-3.0410.3241420.23821305144793
3.041-3.27570.2581550.20241350150595
3.2757-3.60530.21611530.17591361151497
3.6053-4.12670.20911600.16661387154797
4.1267-5.19840.17581540.15761382153696
5.1984-49.92020.18981570.16941414157195

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