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- PDB-8bpz: Crystal structure of YopR -

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Basic information

Entry
Database: PDB / ID: 8bpz
TitleCrystal structure of YopR
ComponentsSPbeta prophage-derived uncharacterized protein YopR
KeywordsDNA BINDING PROTEIN / yopR / phage-repressor / recombinase
Function / homology: / : / MrpR, N-terminal core-binding domain / MrpR, C-terminal catalytic domain / DNA breaking-rejoining enzyme, catalytic core / DNA binding / SPbeta prophage-derived uncharacterized protein YopR
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGallego del Sol, F. / Marina, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN) Spain
CitationJournal: Cell Host Microbe / Year: 2023
Title: Characterization of a unique repression system present in arbitrium phages of the SPbeta family.
Authors: Brady, A. / Cabello-Yeves, E. / Gallego Del Sol, F. / Chmielowska, C. / Mancheno-Bonillo, J. / Zamora-Caballero, S. / Omer, S.B. / Torres-Puente, M. / Eldar, A. / Quiles-Puchalt, N. / Marina, A. / Penades, J.R.
History
DepositionNov 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPbeta prophage-derived uncharacterized protein YopR


Theoretical massNumber of molelcules
Total (without water)37,6331
Polymers37,6331
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.081, 109.081, 53.908
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein SPbeta prophage-derived uncharacterized protein YopR


Mass: 37633.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: yopR, BSU20790 / Production host: Escherichia coli (E. coli) / References: UniProt: O34558
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 30.00 % w/v Polyethylene glycol 4,000, 100 mM tri-Sodium citrate; pH 5.6, 100 mM Ammonium sulfate3/D

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.2→94.47 Å / Num. obs: 19078 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rpim(I) all: 0.018 / Rrim(I) all: 0.077 / Net I/σ(I): 23 / Num. measured all: 360632
Reflection shellResolution: 2.2→2.32 Å / % possible obs: 100 % / Redundancy: 20.1 % / Num. measured all: 55510 / Num. unique obs: 2767 / CC1/2: 0.985 / Rpim(I) all: 0.099 / Rrim(I) all: 0.445 / Net I/σ(I) obs: 7

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMACv7.0.28refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BJV

8bjv


Resolution: 2.2→94.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 13.978 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24861 1479 7.8 %RANDOM
Rwork0.19547 ---
obs0.19967 17599 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.647 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å2-0 Å2
3----1.36 Å2
Refinement stepCycle: 1 / Resolution: 2.2→94.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 0 98 2706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022679
X-RAY DIFFRACTIONr_bond_other_d00.022539
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9773613
X-RAY DIFFRACTIONr_angle_other_deg3.7335911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.58325.156128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67615529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2271513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022938
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02527
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0925.6981297
X-RAY DIFFRACTIONr_mcbond_other4.06878.5111296
X-RAY DIFFRACTIONr_mcangle_it4.8338.5251622
X-RAY DIFFRACTIONr_mcangle_other4.84651623
X-RAY DIFFRACTIONr_scbond_it5.11551382
X-RAY DIFFRACTIONr_scbond_other5.1291383
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4671987
X-RAY DIFFRACTIONr_long_range_B_refined5.4033091
X-RAY DIFFRACTIONr_long_range_B_other5.3773076
X-RAY DIFFRACTIONr_rigid_bond_restr4.33632672
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded28.39852629
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 118 -
Rwork0.245 1301 -
obs--99.93 %
Refinement TLS params.Method: refined / Origin x: -7.5507 Å / Origin y: -41.6345 Å / Origin z: 9.7862 Å
111213212223313233
T0.0239 Å20.0042 Å2-0.0062 Å2-0.0115 Å2-0.0009 Å2--0.0201 Å2
L0.2013 °20.0087 °20.0544 °2-0.2138 °2-0.058 °2--0.0344 °2
S0.0091 Å °0.0033 Å °0.0356 Å °0.0017 Å °-0.0242 Å °-0.0422 Å °0.0109 Å °0.0069 Å °0.0151 Å °

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