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Yorodumi- PDB-2r0x: Crystal structure of a putative flavin reductase (ycdh, hs_1225) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r0x | ||||||
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Title | Crystal structure of a putative flavin reductase (ycdh, hs_1225) from haemophilus somnus 129pt at 1.06 A resolution | ||||||
Components | Possible flavin reductase | ||||||
Keywords | OXIDOREDUCTASE / Split barrel-like / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haemophilus somnus 129PT (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.06 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative flavin reductase (YP_719437.1) from Haemophilus somnus 129PT at 1.06 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. CRYSTAL STRUCTURE PACKING SUGGESTS THAT THE BIOLOGICALLY RELEVANT FORM IS A DIMER. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. | ||||||
Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r0x.cif.gz | 85.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r0x.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 2r0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r0x_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 2r0x_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 2r0x_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 2r0x_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/2r0x ftp://data.pdbj.org/pub/pdb/validation_reports/r0/2r0x | 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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Unit cell |
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Details | SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 17460.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus somnus 129PT (bacteria) / Species: Histophilus somni / Strain: 129Pt / Gene: YP_719437.1, ycdH / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q0I3S1 | ||||||
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#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: NANODROP, 2.0M Ammonium sulfate, 0.1M Sodium acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97925, 0.97898 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 2007 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.06→23.402 Å / Num. obs: 54635 / % possible obs: 98.9 % / Biso Wilson estimate: 6.164 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.34 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.06→23.402 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.07 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.032 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUE 42 WAS NOT MODELED. 4. ACETATE ION AND SULFATE ION FROM CRYSTALLIZATION AND ETHYLENE GLYCOL (EDO) FROM CRYO SOLUTION ARE MODELED.
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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: 9.358 Å2
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Refinement step | Cycle: LAST / Resolution: 1.06→23.402 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.06→1.088 Å / Total num. of bins used: 20
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