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- PDB-6ipx: Crystal structure of the apo form transcription factor -

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Basic information

Entry
Database: PDB / ID: 6ipx
TitleCrystal structure of the apo form transcription factor
ComponentsAimR transcriptional regulator
KeywordsTRANSCRIPTION REGULATOR / a Virus protein / VIRUS
Function / homology: / latency-replication decision / AimR transcriptional regulator
Function and homology information
Biological speciesBacillus phage SPbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.634 Å
AuthorsOy, S.Y. / Zhen, X. / Zhou, H. / Ding, W.
CitationJournal: Protein Cell / Year: 2019
Title: Structural basis of AimP signaling molecule recognition by AimR in Spbeta group of bacteriophages.
Authors: Zhen, X. / Zhou, H. / Ding, W. / Zhou, B. / Xu, X. / Perculija, V. / Chen, C.J. / Chang, M.X. / Choudhary, M.I. / Ouyang, S.
History
DepositionNov 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 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)91,6992
Polymers91,6992
Non-polymers00
Water0
1
A: AimR transcriptional regulator

B: AimR transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)91,6992
Polymers91,6992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x+1/2,-y+1/2,-z+21
Buried area1550 Å2
ΔGint-15 kcal/mol
Surface area36020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.460, 214.710, 33.700
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: 45849.477 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) / Strain (production host): BL21(DE3) / References: UniProt: O64094

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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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 4K, 50 mM magnesium acetate / Temp details: 289.15K

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97981 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97981 Å / Relative weight: 1
ReflectionResolution: 2.634→107.355 Å / Num. obs: 49620 / % possible obs: 99.22 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 2
Reflection shellResolution: 2.63→2.7 Å / Rmerge(I) obs: 0.075 / Num. unique obs: 1866 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IM2

6im2
PDB Unreleased entry


Resolution: 2.634→107.355 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 0 / Phase error: 31.4
RfactorNum. reflection% reflection
Rfree0.2821 3697 7.45 %
Rwork0.2295 --
obs0.2334 49620 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.634→107.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6415 0 0 0 6415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016531
X-RAY DIFFRACTIONf_angle_d1.38788
X-RAY DIFFRACTIONf_dihedral_angle_d8.4234006
X-RAY DIFFRACTIONf_chiral_restr0.067966
X-RAY DIFFRACTIONf_plane_restr0.0081123
LS refinement shellHighest resolution: 2.634 Å /
Rfactor% reflection
Rfree0.28 -
Rwork0.23 -
obs-99.83 %
Refinement TLS params.Method: refined / Origin x: 29.7604 Å / Origin y: 29.0402 Å / Origin z: 44.0181 Å
111213212223313233
T0.4179 Å2-0.0461 Å2-0.0131 Å2-0.4268 Å20.0678 Å2--0.4628 Å2
L0.1047 °20.0899 °20.0361 °2--0.0136 °20.0671 °2---0.0063 °2
S0.0461 Å °-0.0616 Å °-0.1076 Å °0.0231 Å °-0.0389 Å °-0.0778 Å °-0.1098 Å °-0.0218 Å °-0 Å °
Refinement TLS groupSelection details: all

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