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Yorodumi- PDB-3bo9: Crystal structure of putative nitroalkan dioxygenase (TM0800) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bo9 | ||||||
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Title | Crystal structure of putative nitroalkan dioxygenase (TM0800) from Thermotoga maritima at 2.71 A resolution | ||||||
Components | Putative nitroalkan dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / TM0800 / putative nitroalkan dioxygenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima MSB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.71 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative nitroalkan dioxygenase (TM0800) from Thermotoga maritima at 2.71 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 MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bo9.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bo9.ent.gz | 105.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bo9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/3bo9 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/3bo9 | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: HIS / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 0 - 313 / Label seq-ID: 12 - 325
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35786.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: TM0800 / Plasmid: MH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 References: UniProt: Q9WZQ7, enoyl-[acyl-carrier-protein] reductase (NADH) |
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-Non-polymers , 5 types, 43 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-2PE / #6: 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: 4.63 Å3/Da / Density % sol: 73.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.67 Details: NANODROP, 44.0% PEG 400, 0.2M Lithium sulfate, 0.1M Tris-HCl pH 8.67, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97939, 0.97953 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2007 / Details: Adjustable focusing mirrors in K-B geometry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.71→29.761 Å / Num. obs: 37210 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 67.24 Å2 / Rmerge(I) obs: 0.171 / Rsym value: 0.171 / Net I/σ(I): 3.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 2.71→29.761 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 15.515 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.216 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. PEG 400 (2PE) FRAGMENTS, ETHYLENE GLYCOL (EDO) AND SULFATE IONS ARE MODELED BASED ON CRYSTALLIZATION/CRYO CONDITIONS. 5. THE TWO PHOSPHATES MODELED IN THE ACTIVE SITE ARE LIKELY PART OF MONONUCLEOTIDE FMN (BY SIMILARITY TO 2GJN). HOWEVER, THE DENSITY FOR FULL FMN IS TOO WEAK TO ALLOW RELIABLE REFINEMENT.
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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: 39.802 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→29.761 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.71→2.78 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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