+Open data
-Basic information
Entry | Database: PDB / ID: 7zge | ||||||
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Title | BrxA, BREX phage defence protein | ||||||
Components | BrxA, BREX phage defence protein | ||||||
Keywords | ANTIVIRAL PROTEIN / BREX Phage Defence Bacteriophage Exclusion | ||||||
Function / homology | BrxA / BrxA superfamily / BrxA / Uncharacterized protein Function and homology information | ||||||
Biological species | Escherichia fergusonii ATCC 35469 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Picton, D.M. / Beck, I.N. / Blower, T.R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2021 Title: Crystal structure of the anti-CRISPR repressor Aca2. Authors: Usher, B. / Birkholz, N. / Beck, I.N. / Fagerlund, R.D. / Jackson, S.A. / Fineran, P.C. / Blower, T.R. #1: Journal: Curr Res Struct Biol / Year: 2022 Title: Crystal structure of the BREX phage defence protein BrxA Authors: Beck, I.N. / Picton, D.M. / Blower, T.R. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #3: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zge.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zge.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 7zge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zge_validation.pdf.gz | 439.4 KB | Display | wwPDB validaton report |
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Full document | 7zge_full_validation.pdf.gz | 449.1 KB | Display | |
Data in XML | 7zge_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 7zge_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/7zge ftp://data.pdbj.org/pub/pdb/validation_reports/zg/7zge | HTTPS FTP |
-Related structure data
Related structure data | 7b5jC 3bhwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 22770.404 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia fergusonii ATCC 35469 (bacteria) Strain: ATCC 35469 / DSM 13698 / CCUG 18766 / IAM 14443 / JCM 21226 / LMG 7866 / NBRC 102419 / NCTC 12128 / CDC 0568-73 Gene: EFER_p0021 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7L3Y4 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.52 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M (NH4)2SO4, 0.1 M N-(2-acetamido)iminodiacetic acid (ADA, pH 6.5), 18% v/v PEG Smear High |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→42.53 Å / Num. obs: 37354 / % possible obs: 100 % / Redundancy: 1.9 % / Biso Wilson estimate: 39.51 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2.09→2.15 Å / Rmerge(I) obs: 0.374 / Num. unique obs: 2867 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BHW Resolution: 2.09→42.53 Å / SU ML: 0.3379 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8124 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→42.53 Å
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Refine LS restraints |
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LS refinement shell |
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