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- PDB-8bjv: Crystal structure of YopR -

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Basic information

Entry
Database: PDB / ID: 8bjv
TitleCrystal structure of YopR
ComponentsSPbeta prophage-derived uncharacterized protein YopR
KeywordsDNA BINDING PROTEIN / yopR / phage-repressor / recombinase
Function / homologyMrpR, 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 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 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
B: SPbeta prophage-derived uncharacterized protein YopR
C: SPbeta prophage-derived uncharacterized protein YopR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1756
Polymers112,8993
Non-polymers2763
Water4,071226
1
A: SPbeta prophage-derived uncharacterized protein YopR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7252
Polymers37,6331
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SPbeta prophage-derived uncharacterized protein YopR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7252
Polymers37,6331
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SPbeta prophage-derived uncharacterized protein YopR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7252
Polymers37,6331
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.912, 107.750, 52.870
Angle α, β, γ (deg.)90.00, 90.80, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein SPbeta prophage-derived uncharacterized protein YopR


Mass: 37633.016 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: yopR, BSU20790 / Production host: Escherichia coli (E. coli) / References: UniProt: O34558
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 20 % w/v Polyethylene glycol 6,000 100 mM tri-Sodium citrate; pH 5.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.2→93.22 Å / Num. obs: 50520 / % possible obs: 95.6 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Net I/σ(I): 13.8 / Num. measured all: 306236
Reflection shellResolution: 2.2→2.32 Å / % possible obs: 75.6 % / Redundancy: 3.8 % / Num. measured all: 21760 / Num. unique obs: 5767 / CC1/2: 0.816 / Rpim(I) all: 0.323 / Rrim(I) all: 0.648 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC7.0.028refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B6J

8b6j


Resolution: 2.2→93.22 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 17.138 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25437 3659 7.2 %RANDOM
Rwork0.21613 ---
obs0.21899 46857 95.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.751 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å20.74 Å2
2--0.78 Å20 Å2
3----1.1 Å2
Refinement stepCycle: 1 / Resolution: 2.2→93.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7807 0 18 226 8051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.027962
X-RAY DIFFRACTIONr_bond_other_d0.0020.027582
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.97810713
X-RAY DIFFRACTIONr_angle_other_deg0.969317623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.695968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.224.946372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.044151568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4081540
X-RAY DIFFRACTIONr_chiral_restr0.0870.21225
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028669
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021571
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_it2.0544.1333857
X-RAY DIFFRACTIONr_mcbond_other2.0524.1323856
X-RAY DIFFRACTIONr_mcangle_it3.3376.1914818
X-RAY DIFFRACTIONr_mcangle_other3.3376.1924819
X-RAY DIFFRACTIONr_scbond_it2.1474.4044105
X-RAY DIFFRACTIONr_scbond_other2.1454.4044105
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6396.4735892
X-RAY DIFFRACTIONr_long_range_B_refined5.44647.589258
X-RAY DIFFRACTIONr_long_range_B_other5.44647.5859259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A217700.07
12B217700.07
21A216720.08
22C216720.08
31B217220.07
32C217220.07
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 180 -
Rwork0.343 2497 -
obs--69.21 %
Refinement TLS params.

Method: refined / 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)
10.2639-0.0596-0.16940.0635-0.06120.3731-0.04730.020.0694-0.00480.0026-0.0660.1175-0.12140.04470.0889-0.075-0.00310.1099-0.00350.069566.012622.221810.1495
20.53460.32970.14540.42220.27210.1927-0.0029-0.1466-0.1265-0.1727-0.07460.0197-0.1453-0.05760.07750.19820.0593-0.04410.05760.03380.076178.7315-14.39719.674
30.1453-0.03470.18690.3423-0.10940.32630.00990.05020.06270.033-0.05330.11020.04960.17240.04350.03770.03910.01560.1804-0.00760.075340.7496-7.30769.3481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 320
2X-RAY DIFFRACTION2B0 - 320
3X-RAY DIFFRACTION3C0 - 320

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