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Yorodumi- PDB-4e0a: Crystal Structure of the mutant F44R BH1408 protein from Bacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e0a | ||||||
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Title | Crystal Structure of the mutant F44R BH1408 protein from Bacillus halodurans, Northeast Structural Genomics Consortium (NESG) Target BhR182 | ||||||
Components | BH1408 protein | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å | ||||||
Authors | Kuzin, A. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target BhR182 Authors: Kuzin, A. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e0a.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e0a.ent.gz | 119.8 KB | Display | PDB format |
PDBx/mmJSON format | 4e0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e0a_validation.pdf.gz | 464.8 KB | Display | wwPDB validaton report |
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Full document | 4e0a_full_validation.pdf.gz | 465.8 KB | Display | |
Data in XML | 4e0a_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 4e0a_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/4e0a ftp://data.pdbj.org/pub/pdb/validation_reports/e0/4e0a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | dimer,40.06 kD,96.8% |
-Components
#1: Protein | Mass: 19118.080 Da / Num. of mol.: 2 / Mutation: F44R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125 Gene: BH1408 / References: UniProt: Q9KD11 #2: Chemical | #3: Chemical | ChemComp-ACY / | #4: Chemical | #5: 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: 2.01 Å3/Da / Density % sol: 38.95 % |
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Crystal grow | Temperature: 293 K / pH: 5.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.2M NH4-Acetate, 0.1M Bis Tris, 25% PEG 3350, MICROBATCH UNDER OIL, TEMPERATURE 293 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.5 Å / Num. obs: 48794 / % possible obs: 88.3 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.1 / % possible all: 39.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.801→28.5 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.2 / σ(F): 0.12 / Phase error: 23.26 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.182 Å2 / ksol: 0.403 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.801→28.5 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.7873 Å / Origin y: 56.6884 Å / Origin z: 6.7758 Å
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Refinement TLS group | Selection details: all |