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Yorodumi- PDB-3fya: Crystal Structure of an R35A mutant of the Restriction-Modificati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fya | ||||||
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Title | Crystal Structure of an R35A mutant of the Restriction-Modification Controller Protein C.Esp1396I | ||||||
Components | Regulatory protein | ||||||
Keywords | TRANSCRIPTION REGULATOR / transcriptional regulator / helix-turn-helix / Restriction-modification | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | ||||||
Authors | Ball, N.J. / McGeehan, J.E. / Thresh, S.J. / Streeter, S.D. / Kneale, G.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Structure of the restriction-modification controller protein C.Esp1396I. Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E. #1: Journal: Nucleic Acids Res. / Year: 2008 Title: Structural analysis of the genetic switch that regulates the expression of restriction-modification genes Authors: McGeehan, J.E. / Streeter, S.D. / Thresh, S. / Ball, N. / Ravelli, R.B. / Kneale, G.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fya.cif.gz | 42.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fya.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 3fya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fya_validation.pdf.gz | 431.2 KB | Display | wwPDB validaton report |
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Full document | 3fya_full_validation.pdf.gz | 436.8 KB | Display | |
Data in XML | 3fya_validation.xml.gz | 8 KB | Display | |
Data in CIF | 3fya_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/3fya ftp://data.pdbj.org/pub/pdb/validation_reports/fy/3fya | HTTPS FTP |
-Related structure data
Related structure data | 3g5gC 3clcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
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-Components
#1: Protein | Mass: 11324.147 Da / Num. of mol.: 2 / Mutation: R35A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter sp. (bacteria) / Strain: RFL1396 / Gene: esp1396IC / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q8GGH0 |
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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: 2.03 Å3/Da / Density % sol: 39.41 % |
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Crystal grow | Temperature: 277 K / Method: precipitation / pH: 8 Details: 150 mM NaCl, 40 mM Tris-HCl, 5 % w/v glycerol, 2.5 mM CaCl2, pH 8.0, precipitation, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.952→41.959 Å / Num. all: 3840 / Num. obs: 3839 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 86 Å2 / Rmerge(I) obs: 0.263 / Rsym value: 0.263 / Net I/σ(I): 1.394 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CLC Resolution: 3→35.69 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.248 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.811 / SU B: 50.745 / SU ML: 0.406 / SU R Cruickshank DPI: 0.453 / SU Rfree: 0.486 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.28 Å2 / Biso mean: 56.744 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 3→35.69 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 524 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.001→3.078 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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