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- PDB-8i2k: Crystal structure of transcriptional regulator pvrA from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 8i2k
TitleCrystal structure of transcriptional regulator pvrA from Pseudomonas aeruginosa.
ComponentsPutative transcriptional regulator, TetR family
KeywordsDNA BINDING PROTEIN / Transcriptional regulator
Function / homology
Function and homology information


Tetracyclin repressor-like, C-terminal domain (WHG) / Tetracyclin repressor-like, C-terminal domain / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Putative transcriptional regulator, TetR family
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.303 Å
AuthorsPramanik, A. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: To Be Published
Title: Crystal structure of transcriptional regulator pvrA from Pseudomonas aeruginosa.
Authors: Pramanik, A. / Datta, S.
History
DepositionJan 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative transcriptional regulator, TetR family
B: Putative transcriptional regulator, TetR family


Theoretical massNumber of molelcules
Total (without water)50,1442
Polymers50,1442
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-27 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.298, 96.584, 104.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative transcriptional regulator, TetR family


Mass: 25071.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: PA14_25800 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0H2ZBS8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3000, 100mM Tris, 200mM Nacl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Oct 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.3→31.96 Å / Num. obs: 21122 / % possible obs: 99.2 % / Redundancy: 18.7 % / CC1/2: 0.999 / Net I/σ(I): 27.8
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 2059 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
PHENIXv1.14refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
AutoSolphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.303→22.368 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.49 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.254 1967 9.41 %
Rwork0.1918 --
obs0.1975 20894 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.303→22.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 0 255 3523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123339
X-RAY DIFFRACTIONf_angle_d1.2334481
X-RAY DIFFRACTIONf_dihedral_angle_d2.7152021
X-RAY DIFFRACTIONf_chiral_restr0.052469
X-RAY DIFFRACTIONf_plane_restr0.009578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.303-2.36010.2711260.19031265X-RAY DIFFRACTION94
2.3601-2.42380.26831480.18151300X-RAY DIFFRACTION96
2.4238-2.49510.28491360.19181336X-RAY DIFFRACTION97
2.4951-2.57550.25741390.18191307X-RAY DIFFRACTION98
2.5755-2.66740.25831350.18731342X-RAY DIFFRACTION98
2.6674-2.7740.27841350.18781336X-RAY DIFFRACTION98
2.774-2.90.25741370.19771342X-RAY DIFFRACTION98
2.9-3.05260.25941390.20231361X-RAY DIFFRACTION99
3.0526-3.24330.26191440.1921342X-RAY DIFFRACTION99
3.2433-3.49280.24981460.19471368X-RAY DIFFRACTION99
3.4928-3.84270.22381470.18521368X-RAY DIFFRACTION100
3.8427-4.39510.28461450.18051390X-RAY DIFFRACTION100
4.3951-5.52360.24681410.18631408X-RAY DIFFRACTION100
5.5236-22.3680.22341490.21481462X-RAY DIFFRACTION99

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