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- PDB-4z59: HipB-O4 20mer complex -

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Basic information

Entry
Database: PDB / ID: 4z59
TitleHipB-O4 20mer complex
Components
  • Antitoxin HipB
  • DNA (5'-D(*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*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 / 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
DNA / DNA (> 10) / Antitoxin HipB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)14,1942
Polymers14,1942
Non-polymers00
Water2,558142
1
A: Antitoxin HipB
B: DNA (5'-D(*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)-3')

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


Theoretical massNumber of molelcules
Total (without water)28,3884
Polymers28,3884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
Buried area7140 Å2
ΔGint-53 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.370, 127.370, 127.370
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-136-

HOH

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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*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)-3') / Operator 4 of hiBA operon


Mass: 6133.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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 7, 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: 2.3→50 Å / Num. obs: 16312 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 19.38 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.009 / Net I/av σ(I): 43.152 / Net I/σ(I): 11.5 / Num. measured all: 312178
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3416.40.7557960.7221100
2.34-2.3816.50.7967940.7451100
2.38-2.4316.60.6027890.757199.9
2.43-2.4816.40.5998000.7981100
2.48-2.5316.40.4527850.8071100
2.53-2.5916.50.3988010.8481100
2.59-2.6616.70.3937970.871100
2.66-2.7317.50.3287940.865199.7
2.73-2.8118.10.2687940.9131100
2.81-2.918.80.2328120.945199.9
2.9-319.90.1918121.0061100
3-3.1220.80.1438091.0131100
3.12-3.2621.60.0958001.1241100
3.26-3.4421.80.0728091.2041100
3.44-3.65220.0598181.2241100
3.65-3.93220.0478281.1891100
3.93-4.3321.70.0398321.2441100
4.33-4.9521.70.0368291.2341100
4.95-6.2421.30.0368661.0831100
6.24-5019.30.0259471.0941100

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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: 2.3→45.032 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8997 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 15.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1819 1451 10 %
Rwork0.1525 13060 -
obs0.1555 14511 89.16 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.74 Å2 / Biso mean: 23.5411 Å2 / Biso min: 4.18 Å2
Refinement stepCycle: final / Resolution: 2.3→45.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms565 407 0 142 1114
Biso mean--0 35.8 -
Num. residues----91
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011038
X-RAY DIFFRACTIONf_angle_d1.5621489
X-RAY DIFFRACTIONf_chiral_restr0.077171
X-RAY DIFFRACTIONf_plane_restr0.006121
X-RAY DIFFRACTIONf_dihedral_angle_d23.095416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.38250.24631160.19481042115873
2.3825-2.47790.27331280.19521153128181
2.4779-2.59060.23991340.18231206134085
2.5906-2.72720.21551380.18051242138087
2.7272-2.8980.18021450.17911300144590
2.898-3.12180.2171500.17081351150193
3.1218-3.43580.15271500.13591349149993
3.4358-3.93270.16081550.12341405156095
3.9327-4.95380.13421600.11471431159196
4.9538-45.04070.17151750.1621581175698
Refinement TLS params.Method: refined / Origin x: 16.9301 Å / Origin y: 42.6362 Å / Origin z: 14.7597 Å
111213212223313233
T0.0513 Å20.0344 Å20.0061 Å2-0.0491 Å2-0.0005 Å2--0.0764 Å2
L0.0239 °2-0.0017 °20.0107 °2-0.0053 °2-0.0036 °2--0.0142 °2
S-0.0161 Å °-0.0335 Å °0.0601 Å °0.0099 Å °0.0076 Å °-0.0264 Å °-0.012 Å °0.0003 Å °-0.0215 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:74 OR RESID 101:184 ) ) OR ( CHAIN B AND ( RESID 101:157 OR RESID 1:20 ) )A4 - 74
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:74 OR RESID 101:184 ) ) OR ( CHAIN B AND ( RESID 101:157 OR RESID 1:20 ) )A101 - 184
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:74 OR RESID 101:184 ) ) OR ( CHAIN B AND ( RESID 101:157 OR RESID 1:20 ) )B101 - 157
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:74 OR RESID 101:184 ) ) OR ( CHAIN B AND ( RESID 101:157 OR RESID 1:20 ) )B1 - 20

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