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Yorodumi- PDB-2gag: Heteroteterameric sarcosine: structure of a diflavin metaloenzyme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gag | ||||||
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Title | Heteroteterameric sarcosine: structure of a diflavin metaloenzyme at 1.85 a resolution | ||||||
Components | (heterotetrameric sarcosine oxidase ...) x 4 | ||||||
Keywords | OXIDOREDUCTASE / Sarcosine oxidase / Flavoenzyme / Electron transfer / Folate-methylating enzyme | ||||||
Function / homology | Function and homology information sarcosine oxidase (5,10-methylenetetrahydrofolate-forming) / sarcosine catabolic process / sarcosine oxidase activity / tetrahydrofolate metabolic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Chen, Z.W. / Hassan-Abdulah, A. / Zhao, G. / Jorns, M.S. / Mathews, F.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Heterotetrameric sarcosine oxidase: structure of a diflavin metalloenzyme at 1.85 a resolution. Authors: Chen, Z.W. / Hassan-Abdulah, A. / Zhao, G. / Jorns, M.S. / Mathews, F.S. #1: Journal: Protein Expr.Purif. / Year: 2005 Title: Cloning, expression and crystallization of heterotetrameric sarcosine oxidase from Pseudomonas maltophilia | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gag.cif.gz | 365.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gag.ent.gz | 284.9 KB | Display | PDB format |
PDBx/mmJSON format | 2gag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/2gag ftp://data.pdbj.org/pub/pdb/validation_reports/ga/2gag | HTTPS FTP |
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-Related structure data
Related structure data | 2gahSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a heterotetramer. |
-Components
-Heterotetrameric sarcosine oxidase ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 103218.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Gene: soxA / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q3ZDQ8 |
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#2: Protein | Mass: 44117.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Gene: soxB / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 63146664, UniProt: Q3ZDR0*PLUS |
#3: Protein | Mass: 22235.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Gene: soxG / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 63146667, UniProt: Q3ZDQ7*PLUS |
#4: Protein | Mass: 11395.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Gene: soxD / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q3ZDQ9 |
-Non-polymers , 8 types, 1487 molecules
#5: Chemical | #6: Chemical | ChemComp-NAD / | #7: Chemical | ChemComp-GOL / | #8: Chemical | ChemComp-SO3 / | #9: Chemical | ChemComp-FAD / | #10: Chemical | ChemComp-FMN / | #11: Chemical | ChemComp-ZN / | #12: 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: 2.64 Å3/Da / Density % sol: 53.44 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 17% PEG 20000, 0.1M Tris, 0.04M sodium fuorate and 0.01M sodium sulfite., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2004 |
Radiation | Monochromator: APS BEAMLINE 14 BMC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. all: 164316 / Num. obs: 157579 / % possible obs: 95.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.7 / Num. unique all: 14815 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2GAH Resolution: 1.85→40 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1117856.93 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 30.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→40 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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