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- PDB-9f36: Crystal estructure of AimR from ATCC13952 phage -

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Basic information

Entry
Database: PDB / ID: 9f36
TitleCrystal estructure of AimR from ATCC13952 phage
ComponentsArbitrium receptor from ATCC13952 phage
KeywordsDNA BINDING PROTEIN / Arbitrium system / antiterminator
Function / homologyPHOSPHATE ION / :
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGallego del Sol, F. / Marina, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Crystal estructure of AimR from ATCC13952 phage
Authors: Gallego del Sol, F. / Marina, A.
History
DepositionApr 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arbitrium receptor from ATCC13952 phage
B: Arbitrium receptor from ATCC13952 phage
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6993
Polymers90,6042
Non-polymers951
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-19 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.989, 150.767, 67.335
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Arbitrium receptor from ATCC13952 phage


Mass: 45301.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: KS08_10720 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U4KS82
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1M Ammonium dihydrogen phosphate 0.1M NaCitrate pH 5.6

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Data collection

DiffractionMean temperature: 290 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.058→75.38 Å / Num. obs: 52043 / % possible obs: 99.3 % / Redundancy: 11.2 % / CC1/2: 0.999 / Net I/σ(I): 12.7
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 3679 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→75.38 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24707 1906 -RANDOM
Rwork0.19266 ---
obs0.19529 36403 99.97 %-
Displacement parametersBiso mean: 73.572 Å2
Baniso -1Baniso -2Baniso -3
1-7.51 Å20 Å20 Å2
2---3.01 Å20 Å2
3----4.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→75.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5665 0 5 66 5736
LS refinement shellResolution: 2.3→2.36 Å /
Rfactor% reflection
Rfree0.462 -
Rwork0.369 -
obs-99.93 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06680.05480.43530.04680.38213.573-0.0413-0.0123-0.0362-0.01230.02290.3049-0.03620.30490.01840.20850.01080.03990.0310.03080.1775-23.38729.5431-23.6606
20.4666-0.28780.6680.9709-1.32642.5518-0.0380.0927-0.00690.0927-0.11530.2021-0.00690.20210.15330.27520.00910.08920.0210.01320.2991-22.302-27.0382-21.6695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 386
2X-RAY DIFFRACTION2B46 - 386

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