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- PDB-6jg5: Crystal structure of AimR -

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Basic information

Entry
Database: PDB / ID: 6jg5
TitleCrystal structure of AimR
ComponentsAimR transcriptional regulator
KeywordsPEPTIDE BINDING PROTEIN / AimR / Apo / HTH
Function / homology: / AimR transcriptional regulator-like / latency-replication decision / AimR transcriptional regulator
Function and homology information
Biological speciesBacillus phage SPbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.221 Å
AuthorsGuan, Z.Y. / Pei, K. / Zou, T.T.
CitationJournal: Cell Discov / Year: 2019
Title: Structural insights into DNA recognition by AimR of the arbitrium communication system in the SPbeta phage.
Authors: Guan, Z.Y. / Pei, K. / Wang, J. / Cui, Y.Q. / Zhu, X. / Su, X. / Zhou, Y.B. / Zhang, D.L. / Tang, C. / Yin, P. / Liu, Z. / Zou, T.T.
History
DepositionFeb 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: 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: AimR transcriptional regulator
B: AimR transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)93,1512
Polymers93,1512
Non-polymers00
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-14 kcal/mol
Surface area35620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.302, 219.429, 33.494
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein AimR transcriptional regulator / Arbitrium communication peptide receptor / YopK protein


Mass: 46575.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPbeta (virus) / Gene: aimR, yopK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O64094
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Sodium cacodylate, PEG 8000, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 42901 / % possible obs: 99.1 % / Redundancy: 6.4 % / Net I/σ(I): 10.9
Reflection shellResolution: 2.22→2.29 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14rc3_3206: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XYB

5xyb


Resolution: 2.221→49.537 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 2119 4.95 %
Rwork0.1962 --
obs0.1983 42839 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.221→49.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 0 329 6753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096540
X-RAY DIFFRACTIONf_angle_d0.9568800
X-RAY DIFFRACTIONf_dihedral_angle_d23.2052488
X-RAY DIFFRACTIONf_chiral_restr0.056968
X-RAY DIFFRACTIONf_plane_restr0.0051126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2211-2.27280.28511240.21612493X-RAY DIFFRACTION94
2.2728-2.32960.27491390.21632661X-RAY DIFFRACTION100
2.3296-2.39260.29671450.222759X-RAY DIFFRACTION100
2.3926-2.4630.27761180.22342661X-RAY DIFFRACTION100
2.463-2.54250.28991460.21782716X-RAY DIFFRACTION100
2.5425-2.63330.30881410.23292691X-RAY DIFFRACTION100
2.6333-2.73880.26831580.21782656X-RAY DIFFRACTION99
2.7388-2.86340.2791430.20742668X-RAY DIFFRACTION98
2.8634-3.01430.27421400.21582719X-RAY DIFFRACTION99
3.0143-3.20320.27821480.20952678X-RAY DIFFRACTION99
3.2032-3.45040.28211260.20412763X-RAY DIFFRACTION100
3.4504-3.79760.19671190.19012788X-RAY DIFFRACTION100
3.7976-4.34680.19131610.15972688X-RAY DIFFRACTION98
4.3468-5.47540.191660.17122820X-RAY DIFFRACTION100
5.4754-49.54880.21491450.18862959X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -0.324 Å / Origin y: 41.9734 Å / Origin z: 2.5981 Å
111213212223313233
T0.1259 Å20.0478 Å2-0.0109 Å2-0.0996 Å20.0195 Å2--0.1181 Å2
L0.3161 °2-0.1399 °20.0364 °2-0.0837 °2-0.0971 °2---0.1236 °2
S-0.0125 Å °-0.0138 Å °0.1227 Å °0.0594 Å °-0.019 Å °-0.1817 Å °0.0586 Å °-0.0555 Å °-0.0252 Å °
Refinement TLS groupSelection details: all

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