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Yorodumi- PDB-3jsj: Crystal structure of a putative tetr-transcriptional regulator (s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jsj | ||||||
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Title | Crystal structure of a putative tetr-transcriptional regulator (sav143) from streptomyces avermitilis ma-4680 at 2.10 A resolution | ||||||
Components | Putative TetR-family transcriptional regulator | ||||||
Keywords | TRANSCRIPTION / Dna-binding / transcription regulation / bacterial regulatory proteins / dna/rna-binding 3-helical bundle fold / helix turn helix motif / hth motif / transcription regulator / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avermitilis MA-4680 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Putative transcriptional regulator (NP_821317.1) from Streptomyces avermitilis MA-4680 at 2.10 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jsj.cif.gz | 156 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jsj.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 3jsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jsj_validation.pdf.gz | 460.4 KB | Display | wwPDB validaton report |
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Full document | 3jsj_full_validation.pdf.gz | 466.4 KB | Display | |
Data in XML | 3jsj_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 3jsj_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/3jsj ftp://data.pdbj.org/pub/pdb/validation_reports/js/3jsj | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | REMARK 300 REMARK 300 REMARK: ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH REMARK 300 STATIC LIGHT SCATTERING SUGGESTS THAT A TETRAMER IS A REMARK 300 SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. HOWEVER, R REMARK 300 ANALYSIS OF THE CRYSTAL PACKING SUGGESTS THAT A DIMER REMARK 300 IS OLIGOMERIZATION STATE IN THE CRYSTAL. REMARK 300 REMARK 300 BIOMOLECULE: 1,2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 BIOMOLECULE 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 1.18 REMARK 350 TOTAL BURIED SURFACE AREA FOR THE COMPLEX: 3280 A**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 16490 A**2 REMARK 350 GAIN IN SOLVENT FREE ENERGY: -20 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 1.18 REMARK 350 TOTAL BURIED SURFACE AREA FOR THE COMPLEX: 3300 A**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 16620 A**2 REMARK 350 GAIN IN SOLVENT FREE ENERGY: -20 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 |
-Components
#1: Protein | Mass: 20667.891 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis MA-4680 (bacteria) Gene: NP_821317.1, SAV143, SAV_143 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q82RK0 #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Sequence details | SEQUENCE THIE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THIE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.91 Å3/Da / Density % sol: 57.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.3000M magnesium chloride, 16.0000% polyethylene glycol 8000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97809 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2009 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97809 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→29.748 Å / Num. obs: 55159 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.23 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.74 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→29.748 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.532 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.168 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. MAGNESIUM FROM THE CRYSTALLIZATION SOLUTION AND 1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT HAVE BEEN MODELED INTO THE STRUCTURE.
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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: 66.07 Å2 / Biso mean: 21.447 Å2 / Biso min: 4.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.748 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2267 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.155 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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