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- PDB-6lb3: Crystal structure of PA4674 in complex with its operator DNA (18b... -

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Basic information

Entry
Database: PDB / ID: 6lb3
TitleCrystal structure of PA4674 in complex with its operator DNA (18bp) from Pseudomonas aeruginosa
Components
  • DNA (5'-D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3')
  • DNA (5'-D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3')
  • HTH cro/C1-type domain-containing protein
KeywordsANTITOXIN/DNA / Toxin antitoxin system / transcription regulator / DNA binding protein / ANTITOXIN / ANTITOXIN-DNA complex
Function / homology
Function and homology information


Toxin-antitoxin system, antidote protein, HigA / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH cro/C1-type domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsLiu, Y. / Zhang, H. / Gao, Z. / Dong, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)U1732113 China
CitationJournal: To Be Published
Title: Crystal structure of PA4674 in complex with its operator DNA (18bp) from Pseudomonas aeruginosa
Authors: Liu, Y. / Zhang, H. / Gao, Z. / Dong, Y.
History
DepositionNov 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: HTH cro/C1-type domain-containing protein
B: HTH cro/C1-type domain-containing protein
C: HTH cro/C1-type domain-containing protein
D: HTH cro/C1-type domain-containing protein
E: HTH cro/C1-type domain-containing protein
F: HTH cro/C1-type domain-containing protein
G: HTH cro/C1-type domain-containing protein
H: HTH cro/C1-type domain-containing protein
I: DNA (5'-D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3')
J: DNA (5'-D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3')
K: DNA (5'-D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3')
L: DNA (5'-D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3')
M: DNA (5'-D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3')
N: DNA (5'-D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,14816
Polymers130,95614
Non-polymers1922
Water1,09961
1
M: DNA (5'-D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3')
N: DNA (5'-D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)11,0312
Polymers11,0312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HTH cro/C1-type domain-containing protein
B: HTH cro/C1-type domain-containing protein
G: HTH cro/C1-type domain-containing protein
H: HTH cro/C1-type domain-containing protein
I: DNA (5'-D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3')
J: DNA (5'-D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1548
Polymers59,9626
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-102 kcal/mol
Surface area23240 Å2
MethodPISA
3
C: HTH cro/C1-type domain-containing protein
D: HTH cro/C1-type domain-containing protein
E: HTH cro/C1-type domain-containing protein
F: HTH cro/C1-type domain-containing protein
K: DNA (5'-D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3')
L: DNA (5'-D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)59,9626
Polymers59,9626
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-103 kcal/mol
Surface area23180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.284, 95.570, 128.857
Angle α, β, γ (deg.)90.000, 96.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HTH cro/C1-type domain-containing protein


Mass: 12232.791 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: PA4674 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HVC1
#2: DNA chain DNA (5'-D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3')


Mass: 5555.616 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)
#3: DNA chain DNA (5'-D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3')


Mass: 5475.567 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES, 35% MPD, 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.497→50 Å / Num. obs: 47794 / % possible obs: 99.3 % / Redundancy: 6.2 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 20.1
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 2352 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TRB

3trb


Resolution: 2.497→47.201 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 1995 4.22 %
Rwork0.2176 45326 -
obs0.2194 47321 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.02 Å2 / Biso mean: 65.2745 Å2 / Biso min: 37.15 Å2
Refinement stepCycle: final / Resolution: 2.497→47.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5812 1763 10 61 7646
Biso mean--68.58 55.62 -
Num. residues----821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017911
X-RAY DIFFRACTIONf_angle_d1.17911064
X-RAY DIFFRACTIONf_chiral_restr0.061220
X-RAY DIFFRACTIONf_plane_restr0.0071144
X-RAY DIFFRACTIONf_dihedral_angle_d22.2594462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4972-2.55970.36561280.3266293091
2.5597-2.62890.35811440.3052324998
2.6289-2.70620.36681420.3323399
2.7062-2.79350.37441410.2867319298
2.7935-2.89340.31151430.2696326399
2.8934-3.00920.28091430.2673324099
3.0092-3.14610.36181420.2608321599
3.1461-3.3120.30181420.2479323898
3.312-3.51940.26771410.2198321698
3.5194-3.7910.27381450.2243283100
3.791-4.17230.21991450.18743296100
4.1723-4.77560.22261460.17983327100
4.7756-6.01480.231440.20083276100
6.0148-47.2010.21561490.1815336899

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