+Open data
-Basic information
Entry | Database: PDB / ID: 4p86 | ||||||
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Title | Structure of PyrR protein from Bacillus subtilis with GMP | ||||||
Components | Bifunctional protein PyrR | ||||||
Keywords | TRANSFERASE / RNA binding proteins | ||||||
Function / homology | Rossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / GUANOSINE-5'-MONOPHOSPHATE Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Perica, T. / Kondo, Y. / Tiwari, S. / McLaughlin, S. / Steward, A. / Reuter, N. / Clarke, J. / Teichmann, S.A. | ||||||
Citation | Journal: Science / Year: 2014 Title: Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Authors: Perica, T. / Kondo, Y. / Tiwari, S.P. / McLaughlin, S.H. / Kemplen, K.R. / Zhang, X. / Steward, A. / Reuter, N. / Clarke, J. / Teichmann, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p86.cif.gz | 155.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p86.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 4p86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/4p86 ftp://data.pdbj.org/pub/pdb/validation_reports/p8/4p86 | HTTPS FTP |
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-Related structure data
Related structure data | 4p3kC 4p80C 4p81C 4p82C 4p83C 4p84C 1a3cS 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: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 20432.395 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pRSET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 #2: Chemical | ChemComp-5GP / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 25.5% PEG 4000, 0.085 M Na Citrate pH 5.6, 0.17 M Ammonium Acetate, 15% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→54.58 Å / Num. obs: 50228 / % possible obs: 96.4 % / Redundancy: 2.7 % / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.93→1.98 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.4 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1a3c Resolution: 1.93→54.58 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.087 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.145 / 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 mean: 45.056 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→54.58 Å
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Refine LS restraints |
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