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Yorodumi- PDB-3fjy: Crystal structure of a probable MutT1 protein from Bifidobacteriu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fjy | ||||||
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Title | Crystal structure of a probable MutT1 protein from Bifidobacterium adolescentis | ||||||
Components | Probable MutT1 protein | ||||||
Keywords | HYDROLASE / Probable MutT1 protein / Dimer / Protein Structure Initiative II(PSI II) / NYSGXRC / 11181h / Structural Genomics / New York SGX Research Center for Structural Genomics / unknown function | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bifidobacterium adolescentis ATCC 15703 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Palani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a probable MutT1 protein from Bifidobacterium adolescentis Authors: Palani, K. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fjy.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fjy.ent.gz | 120.4 KB | Display | PDB format |
PDBx/mmJSON format | 3fjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/3fjy ftp://data.pdbj.org/pub/pdb/validation_reports/fj/3fjy | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | DIMER |
-Components
#1: Protein | Mass: 41209.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium adolescentis ATCC 15703 (bacteria) Strain: ATCC 15703/DSM 20083 / Gene: BAD_0126, mutT1 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0ZZM4 #2: Chemical | #3: 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: 2.67 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M Ammonium citrate dibasic 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 4, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(III) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. all: 92926 / Num. obs: 92926 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.15→2.28 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1 / Num. unique all: 9289 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 56608.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.1115 Å2 / ksol: 0.360909 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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