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- PDB-4z5h: HipB(S29A)-O2 20mer complex -

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Basic information

Entry
Database: PDB / ID: 4z5h
TitleHipB(S29A)-O2 20mer complex
Components
  • Antitoxin HipB
  • DNA (5'-D(*TP*TP*AP*TP*CP*CP*TP*CP*AP*CP*TP*AP*AP*AP*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: 2.1 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*TP*CP*AP*CP*TP*AP*AP*AP*GP*GP*AP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)14,2322
Polymers14,2322
Non-polymers00
Water2,900161
1
A: Antitoxin HipB
B: DNA (5'-D(*TP*TP*AP*TP*CP*CP*TP*CP*AP*CP*TP*AP*AP*AP*GP*GP*AP*TP*AP*A)-3')

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


Theoretical massNumber of molelcules
Total (without water)28,4654
Polymers28,4654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
Buried area7040 Å2
ΔGint-53 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.714, 127.714, 127.714
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11B-155-

HOH

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Components

#1: Protein Antitoxin HipB


Mass: 8131.316 Da / Num. of mol.: 1 / Fragment: UNP residues 3-74 / Mutation: S29A
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*TP*CP*AP*CP*TP*AP*AP*AP*GP*GP*AP*TP*AP*A)-3') / Operator 2 of hiBA operon


Mass: 6100.994 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.: 161 / 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: Feb 25, 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: 2.1→50 Å / Num. obs: 21371 / % possible obs: 100 % / Redundancy: 22.4 % / Rmerge(I) obs: 0.053 / Χ2: 1.006 / Net I/av σ(I): 69.88 / Net I/σ(I): 15 / Num. measured all: 479223
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1421.60.91410240.7421100
2.14-2.1821.70.81910630.7521100
2.18-2.22220.70210240.8021100
2.22-2.2622.10.60110510.8211100
2.26-2.3122.20.55910530.8111100
2.31-2.3722.50.41610380.8311100
2.37-2.4222.60.33510370.8591100
2.42-2.4922.70.28610520.9251100
2.49-2.5622.90.22110560.9441100
2.56-2.65230.206105311100
2.65-2.7423.10.17210471.021100
2.74-2.8523.10.12810641.0691100
2.85-2.9823.10.09910601.1581100
2.98-3.14230.07510701.2341100
3.14-3.3322.70.0510781.323199.9
3.33-3.5922.70.03910651.3181100
3.59-3.9522.50.03410881.288199.9
3.95-4.5222.20.0311001.203199.7
4.52-5.722.10.02811191.052199.9
5.7-5020.70.02312290.8911100

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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: 2.1→45.154 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8885 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.21 / Phase error: 17.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 927 5 %
Rwork0.1871 17611 -
obs0.1879 18538 86.89 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.97 Å2 / Biso mean: 24.4384 Å2 / Biso min: 7.17 Å2
Refinement stepCycle: final / Resolution: 2.1→45.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms569 405 0 161 1135
Biso mean--0 32.41 -
Num. residues----92
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071031
X-RAY DIFFRACTIONf_angle_d1.2591476
X-RAY DIFFRACTIONf_chiral_restr0.061171
X-RAY DIFFRACTIONf_plane_restr0.003118
X-RAY DIFFRACTIONf_dihedral_angle_d22.246412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.21240.26591170.21652223234079
2.2124-2.3510.22691230.20732339246282
2.351-2.53250.19811240.20392347247183
2.5325-2.78730.2371290.21742442257186
2.7873-3.19060.21731320.20172524265688
3.1906-4.01940.18131450.16752747289294
4.0194-45.16410.18451570.16662989314696

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