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Yorodumi- PDB-3b8l: CRYSTAL STRUCTURE OF A PUTATIVE AROMATIC RING HYDROXYLASE (SARO_3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b8l | ||||||
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Title | CRYSTAL STRUCTURE OF A PUTATIVE AROMATIC RING HYDROXYLASE (SARO_3538) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM AT 1.75 A RESOLUTION | ||||||
Components | Uncharacterized protein | ||||||
Keywords | OXIDOREDUCTASE / PUTATIVE AROMATIC RING HYDROXYLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DI(HYDROXYETHYL)ETHER / SnoaL-like domain-containing protein Function and homology information | ||||||
Biological species | Novosphingobium aromaticivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of NTF2-like protein of unknown function (YP_001165924.1) from Novosphingobium aromaticivorans DSM 12444 at 1.75 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b8l.cif.gz | 207.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b8l.ent.gz | 166.7 KB | Display | PDB format |
PDBx/mmJSON format | 3b8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b8l_validation.pdf.gz | 502.4 KB | Display | wwPDB validaton report |
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Full document | 3b8l_full_validation.pdf.gz | 513.3 KB | Display | |
Data in XML | 3b8l_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 3b8l_validation.cif.gz | 66 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/3b8l ftp://data.pdbj.org/pub/pdb/validation_reports/b8/3b8l | HTTPS FTP |
-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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2 |
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Unit cell |
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 18640.736 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria) Strain: DSM 12444 / Gene: YP_001165924.1, Saro_3538 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A4XEN7 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has protein modification | Y | Sequence details | REMARK 999 SEQUENCE: THE 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: 2.39 Å3/Da / Density % sol: 48.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: NANODROP, 30.0% Glycerol, 5.6% PEG 4000, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0000, 0.9798, 0.9796 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→29.54 Å / Num. obs: 109179 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.44 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.12 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→29.54 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.928 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.098 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GLYCEROL AND POLYETHYLENE GLYCOL WERE MODELED FROM THE CRYSTALLIZATION CONDITIONS.
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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: 21.332 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→29.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.8 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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