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- PDB-7t8k: BrxR from Acinetobacter BREX type I phage restriction system boun... -

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Basic information

Entry
Database: PDB / ID: 7t8k
TitleBrxR from Acinetobacter BREX type I phage restriction system bound to DNA
Components
  • (DNA) x 2
  • BrxR
KeywordsDNA BINDING PROTEIN/DNA / Phage restriction / BREX / DNA binding / regulatory / Acinetobacter / Bacteriophage Exclusion / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homologyWYL domain protein, s026 type / : / WYL domain profile. / WYL domain / WYL domain / DNA / DNA (> 10) / WYL domain-containing protein
Function and homology information
Biological speciesAcinetobacter sp. NEB 394 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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
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 1.2Feb 28, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BrxR
B: BrxR
C: DNA
D: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,59412
Polymers82,1514
Non-polymers4438
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15510 Å2
ΔGint-73 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.586, 71.477, 87.413
Angle α, β, γ (deg.)90.000, 105.130, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 4 or (resid 5...
21(chain B and (resid 3 through 57 or (resid 58...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASP(chain A and (resid 3 through 4 or (resid 5...AA3 - 46 - 7
12LYSLYSLYSLYS(chain A and (resid 3 through 4 or (resid 5...AA58
13ALAALASERSER(chain A and (resid 3 through 4 or (resid 5...AA3 - 2886 - 291
14ALAALASERSER(chain A and (resid 3 through 4 or (resid 5...AA3 - 2886 - 291
15ALAALASERSER(chain A and (resid 3 through 4 or (resid 5...AA3 - 2886 - 291
16ALAALASERSER(chain A and (resid 3 through 4 or (resid 5...AA3 - 2886 - 291
21ALAALALEULEU(chain B and (resid 3 through 57 or (resid 58...BB3 - 576 - 60
22ILEILEILEILE(chain B and (resid 3 through 57 or (resid 58...BB5861
23ALAALALEULEU(chain B and (resid 3 through 57 or (resid 58...BB3 - 2796 - 282
24ALAALALEULEU(chain B and (resid 3 through 57 or (resid 58...BB3 - 2796 - 282
25ALAALALEULEU(chain B and (resid 3 through 57 or (resid 58...BB3 - 2796 - 282

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BrxR


Mass: 33400.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Homodimer / Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Gene: HUK62_18310 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H8SL41

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA


Mass: 7686.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acinetobacter sp. NEB 394 (bacteria)
#3: DNA chain DNA


Mass: 7664.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acinetobacter sp. NEB 394 (bacteria)

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Non-polymers , 3 types, 125 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.04 M Citric acid, 20% w/v PEG 3350, 0.06 M BIS-TRIS propane, pH 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 38735 / % possible obs: 97.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.042 / Rrim(I) all: 0.105 / Χ2: 1.375 / Net I/σ(I): 11.3 / Num. measured all: 239308
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.386.10.61239290.8470.2640.6680.655100
2.38-2.486.20.47739220.9090.2050.520.75999.8
2.48-2.595.90.35839480.9230.160.3930.90799.9
2.59-2.736.40.26639680.960.1130.2891.19399.9
2.73-2.96.50.20839340.9750.0880.2261.22999.7
2.9-3.126.10.15839520.9810.070.1731.54999.5
3.12-3.446.30.12138150.9890.0520.1322.02496.5
3.44-3.936.20.09837030.9920.0430.1082.20692.7
3.93-4.9660.08235770.9930.0370.0912.02789.6
4.96-1006.10.06339870.9970.0270.0681.30997.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.3 Å84.38 Å
Translation2.3 Å84.38 Å

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
HKL-2000data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo BrxR

Resolution: 2.3→64.22 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 1984 5.17 %
Rwork0.1958 36367 -
obs0.1979 38351 95.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.97 Å2 / Biso mean: 55.099 Å2 / Biso min: 30.99 Å2
Refinement stepCycle: final / Resolution: 2.3→64.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 1019 32 117 5578
Biso mean--73.09 51.91 -
Num. residues----613
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1669X-RAY DIFFRACTION5.797TORSIONAL
12B1669X-RAY DIFFRACTION5.797TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.360.32891170.22782118223579
2.36-2.420.28661420.23782584272696
2.42-2.490.26921450.23132665281098
2.49-2.570.28571460.24082666281298
2.57-2.670.32291460.23032681282799
2.67-2.770.27031460.23652675282199
2.77-2.90.33831460.24242701284799
2.9-3.050.27181470.24222686283399
3.05-3.240.27461470.23352677282498
3.24-3.490.30861410.23012608274995
3.49-3.840.25581380.20012519265793
3.84-4.40.21561350.17182478261390
4.4-5.540.18621380.16742538267692
5.54-64.220.16561500.14952771292198

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