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- PDB-8bny: Structure of the tetramerization domain of pLS20 conjugation repr... -

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Basic information

Entry
Database: PDB / ID: 8bny
TitleStructure of the tetramerization domain of pLS20 conjugation repressor Rco
ComponentsImmunity repressor protein
KeywordsDNA BINDING PROTEIN / tetramerization / repressor / conjugation / Gram+
Function / homologyHelix-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 / DNA binding / Immunity repressor protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.429 Å
AuthorsBernardo, N. / Crespo, I. / Meijer, W.J.J. / Boer, D.R.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-77883-C2-2-P Spain
Spanish Ministry of Economy and CompetitivenessFIS2015-72574-EXP Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53.
Authors: Bernardo, N. / Crespo, I. / Cuppari, A. / Meijer, W.J.J. / Boer, D.R.
History
DepositionNov 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunity repressor protein
B: Immunity repressor protein
C: Immunity repressor protein
D: Immunity repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4935
Polymers74,4574
Non-polymers351
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-41 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.328, 36.182, 109.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Immunity repressor protein


Mass: 18614.338 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli B (bacteria) / References: UniProt: E9RIY8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes pH 7.5, 28% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.409→34.36 Å / Num. obs: 18842 / % possible obs: 91.6 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rrim(I) all: 0.044 / Rsym value: 0.039 / Net I/σ(I): 14.5
Reflection shellResolution: 1.409→1.433 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 943 / CC1/2: 0.512 / Rrim(I) all: 0.78 / Rsym value: 0.714

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Processing

Software
NameVersionClassification
autoPROCdata processing
Arcimboldophasing
PHENIX1.12-2829refinement
Cootmodel building
PHENIX1.12-2829model building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.429→34.356 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 41.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 900 4.84 %
Rwork0.2332 17681 -
obs0.234 18581 69.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.83 Å2 / Biso mean: 38.4852 Å2 / Biso min: 11.29 Å2
Refinement stepCycle: final / Resolution: 1.429→34.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 1 62 1255
Biso mean--55.35 38.39 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061209
X-RAY DIFFRACTIONf_angle_d0.7241604
X-RAY DIFFRACTIONf_chiral_restr0.058184
X-RAY DIFFRACTIONf_plane_restr0.003198
X-RAY DIFFRACTIONf_dihedral_angle_d19.739496
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4295-1.5190.3732130.32762827
1.519-1.63630.3382700.3086138733
1.6363-1.8010.32231780.3204343281
1.801-2.06160.3122170.346397695
2.0616-2.59720.30311900.2735420898
2.5972-34.3560.21212320.1871439699
Refinement TLS params.Method: refined / Origin x: -9.7148 Å / Origin y: -4.9982 Å / Origin z: 15.5876 Å
111213212223313233
T0.0449 Å20.0004 Å2-0.0071 Å2-0.0276 Å2-0.038 Å2--0.0559 Å2
L4.6517 °2-0.7031 °2-0.0943 °2-1.5658 °21.0686 °2--2.7582 °2
S0.0954 Å °0.5613 Å °-0.0556 Å °-0.0772 Å °-0.0261 Å °-0.117 Å °-0.2528 Å °0.2187 Å °0.0299 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA125 - 159
2X-RAY DIFFRACTION1allB124 - 157
3X-RAY DIFFRACTION1allC124 - 158
4X-RAY DIFFRACTION1allD124 - 159
5X-RAY DIFFRACTION1allI1 - 84
6X-RAY DIFFRACTION1allJ2

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