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- PDB-8bj6: Crystal structure of YopR -

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Basic information

Entry
Database: PDB / ID: 8bj6
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 / SAD / Resolution: 2.6 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 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)112,3043
Polymers112,3043
Non-polymers00
Water99155
1
A: SPbeta prophage-derived uncharacterized protein YopR


Theoretical massNumber of molelcules
Total (without water)37,4351
Polymers37,4351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SPbeta prophage-derived uncharacterized protein YopR


Theoretical massNumber of molelcules
Total (without water)37,4351
Polymers37,4351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SPbeta prophage-derived uncharacterized protein YopR


Theoretical massNumber of molelcules
Total (without water)37,4351
Polymers37,4351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.682, 108.007, 53.601
Angle α, β, γ (deg.)90.00, 90.36, 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: 37434.516 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 8000, 100 mM Sodium phosphate dibasic/ Citric acid pH 4.2, 200 mM Sodium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 2.6→94.84 Å / Num. obs: 32678 / % possible obs: 98.2 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Net I/σ(I): 12.5 / Num. measured all: 209837
Reflection shellResolution: 2.6→2.74 Å / % possible obs: 94.5 % / Redundancy: 5.8 % / Num. measured all: 26583 / Num. unique obs: 4555 / CC1/2: 0.933 / Rpim(I) all: 0.194 / Rrim(I) all: 0.46 / Net I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMACv7.0refinement
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→94.84 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 32.44 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 1634 5 %RANDOM
Rwork0.21789 ---
obs0.21977 30962 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.128 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å2-0 Å2-0.21 Å2
2--4.12 Å20 Å2
3----2.2 Å2
Refinement stepCycle: 1 / Resolution: 2.6→94.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7802 0 0 55 7857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.027916
X-RAY DIFFRACTIONr_bond_other_d0.0030.027536
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.98710650
X-RAY DIFFRACTIONr_angle_other_deg1.005317511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7785959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69624.959369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.348151492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3281539
X-RAY DIFFRACTIONr_chiral_restr0.080.21217
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028621
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021562
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_it1.9684.9983845
X-RAY DIFFRACTIONr_mcbond_other1.9674.9963844
X-RAY DIFFRACTIONr_mcangle_it3.3847.4884801
X-RAY DIFFRACTIONr_mcangle_other3.3847.494802
X-RAY DIFFRACTIONr_scbond_it1.9465.2084071
X-RAY DIFFRACTIONr_scbond_other1.9465.2094072
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3427.6835850
X-RAY DIFFRACTIONr_long_range_B_refined5.27756.5288727
X-RAY DIFFRACTIONr_long_range_B_other5.27656.5368726
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: tight thermal / Weight position: 0.71

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A26013.61
22B25892.95
33C25884.54
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.515 130 -
Rwork0.369 2152 -
obs--92.65 %
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)
10.17370.2975-0.04970.72750.02260.08680.01230.0349-0.16120.0041-0.0995-0.2406-0.0243-0.13520.08720.07030.0387-0.01050.2366-0.06180.16453.0143-0.233510.0516
20.6087-0.31530.13670.26670.02360.1357-0.12330.0243-0.08590.0090.03320.1556-0.11960.08360.09020.1776-0.0847-0.02340.13520.04140.139127.3262-29.81119.618
31.2180.15450.04170.0238-0.01020.0592-0.0653-0.07370.3999-0.0463-0.00370.04010.13140.03540.0690.31660.09280.06490.02930.00170.158314.09696.98489.759
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 320
2X-RAY DIFFRACTION2B0 - 320
3X-RAY DIFFRACTION3C1 - 320

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