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- PDB-7t8l: BrxR from Acinetobacter BREX type I phage restriction system -

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Basic information

Entry
Database: PDB / ID: 7t8l
TitleBrxR from Acinetobacter BREX type I phage restriction system
ComponentsBrxR
KeywordsDNA BINDING PROTEIN / Phage restriction / BREX / DNA binding / regulatory / Acinetobacter / Bacteriophage Exclusion
Function / homologyWYL domain protein, s026 type / : / WYL domain profile. / WYL domain / WYL domain / WYL domain-containing protein
Function and homology information
Biological speciesAcinetobacter sp. NEB 394 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDoyle, L. / Kaiser, B. / Stoddard, B.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105691 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM140375-01A1 United States
Other private United States
Other private United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system.
Authors: Luyten, Y.A. / Hausman, D.E. / Young, J.C. / Doyle, L.A. / Higashi, K.M. / Ubilla-Rodriguez, N.C. / Lambert, A.R. / Arroyo, C.S. / Forsberg, K.J. / Morgan, R.D. / Stoddard, B.L. / Kaiser, B.K.
History
DepositionDec 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: BrxR
B: BrxR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9618
Polymers67,6152
Non-polymers3466
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-30 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.414, 48.672, 96.005
Angle α, β, γ (deg.)90.000, 102.251, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BrxR


Mass: 33807.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein was expressed and crystallized with only Cysteines, however some of those Cysteines were converted to S-Sulfinocysteines (CSD) due to treatment of the crystals with Hydrogen ...Details: The protein was expressed and crystallized with only Cysteines, however some of those Cysteines were converted to S-Sulfinocysteines (CSD) due to treatment of the crystals with Hydrogen peroxide (supported by very clear electron density). The CSD are only a byproduct of H2O2 treatment during freezing, not originally in the expressed/crystallized protein.
Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Gene: HUK62_18310 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H8SL41
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 10%PEG3000 / 0.1 M Hepes, pH 7.3 / 2% Benz-HCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→63.92 Å / Num. obs: 40089 / % possible obs: 99.5 % / Redundancy: 3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.074 / Rrim(I) all: 0.108 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.8 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
8.94-63.920.0424950.9930.0410.05999.7
2-2.050.31728820.8630.30.43897.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALS2.1.3data reduction
Aimless0.7.4data scaling
pointless1.11.21data scaling
CRANK22.0.229phasing
RefinementMethod to determine structure: SAD / Resolution: 2→63.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.385 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.187 / ESU R Free: 0.169
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2384 2075 5.178 %
Rwork0.1905 38002 -
all0.193 --
obs-40077 99.447 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.848 Å2
Baniso -1Baniso -2Baniso -3
1-1.993 Å2-0 Å20.227 Å2
2---0.75 Å20 Å2
3----1.226 Å2
Refinement stepCycle: LAST / Resolution: 2→63.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 21 157 4550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134507
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154230
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.656145
X-RAY DIFFRACTIONr_angle_other_deg1.2691.5679673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2821.579228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7315667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3061532
X-RAY DIFFRACTIONr_chiral_restr0.0750.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
X-RAY DIFFRACTIONr_nbd_refined0.2070.2814
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.23892
X-RAY DIFFRACTIONr_nbtor_refined0.160.22123
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22198
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2156
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1210.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.215
X-RAY DIFFRACTIONr_nbd_other0.2120.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3780.212
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0320.21
X-RAY DIFFRACTIONr_mcbond_it2.7263.1462239
X-RAY DIFFRACTIONr_mcbond_other2.7253.1442238
X-RAY DIFFRACTIONr_mcangle_it3.8484.7042797
X-RAY DIFFRACTIONr_mcangle_other3.8484.7062798
X-RAY DIFFRACTIONr_scbond_it3.3933.4412268
X-RAY DIFFRACTIONr_scbond_other3.3923.4412269
X-RAY DIFFRACTIONr_scangle_it5.1175.0163348
X-RAY DIFFRACTIONr_scangle_other5.1165.0163349
X-RAY DIFFRACTIONr_lrange_it6.65737.14750
X-RAY DIFFRACTIONr_lrange_other6.65637.1084751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3011350.232744X-RAY DIFFRACTION97.5271
2.052-2.1080.291630.2222716X-RAY DIFFRACTION99.6194
2.108-2.1690.2431410.2032630X-RAY DIFFRACTION99.6046
2.169-2.2360.2391260.2032574X-RAY DIFFRACTION99.4109
2.236-2.3090.2471390.1952478X-RAY DIFFRACTION99.0913
2.309-2.390.2581200.1962439X-RAY DIFFRACTION98.9942
2.39-2.480.2331320.1982290X-RAY DIFFRACTION99.9587
2.48-2.5810.2821340.1982240X-RAY DIFFRACTION99.3305
2.581-2.6960.2141240.192156X-RAY DIFFRACTION99.5633
2.696-2.8270.2511220.22056X-RAY DIFFRACTION99.7253
2.827-2.980.2861190.2041952X-RAY DIFFRACTION99.2333
2.98-3.160.2291200.1911844X-RAY DIFFRACTION99.8983
3.16-3.3780.233800.1941775X-RAY DIFFRACTION100
3.378-3.6470.228770.1931651X-RAY DIFFRACTION99.9422
3.647-3.9940.24820.1761514X-RAY DIFFRACTION99.8124
3.994-4.4630.208760.1551381X-RAY DIFFRACTION100
4.463-5.150.183690.1571212X-RAY DIFFRACTION100
5.15-6.2970.223440.2131048X-RAY DIFFRACTION99.635
6.297-8.8620.308480.198819X-RAY DIFFRACTION99.8848
8.862-63.920.206240.198483X-RAY DIFFRACTION99.8031

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