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Yorodumi- PDB-2pfx: Crystal structure of uncharacterized peroxidase-related protein (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pfx | ||||||
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Title | Crystal structure of uncharacterized peroxidase-related protein (YP_614459.1) from Silicibacter sp. TM1040 at 1.70 A resolution | ||||||
Components | Uncharacterized peroxidase-related protein | ||||||
Keywords | OXIDOREDUCTASE / YP_614459.1 / uncharacterized peroxidase-related protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Silicibacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of uncharacterized peroxidase-related protein (YP_614459.1) from Silicibacter sp. TM1040 at 1.70 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE HEXAMER 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 (0) FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pfx.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pfx.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/2pfx ftp://data.pdbj.org/pub/pdb/validation_reports/pf/2pfx | 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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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 22111.361 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Silicibacter sp. (bacteria) / Strain: TM1040 / Gene: YP_614459.1, TM1040_2465 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GDR9 #2: Chemical | #3: Chemical | ChemComp-PG4 / | #4: Chemical | ChemComp-CL / | #5: 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: 2.49 Å3/Da / Density % sol: 50.67 % |
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Crystal grow | Temperature: 277 K / pH: 4.5 Details: NANODROP, 0.1M NaCl, 30.0% PEG 200, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 4.50 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97908, 0.97929 | ||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 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: 1.7→27.842 Å / Num. obs: 47633 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 5.4 | ||||||||||||
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.437 / % possible all: 100 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→27.84 Å / Num. parameters: 13529 / Num. restraintsaints: 13579 / Cross valid method: FREE R / σ(F): 0 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. ACETATE (ACT) MOLECULES, CL ION AND TETRAETHYLENE GLYCOL (PG4) FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 4. THE SHELXL WAS USED FOR REFINEMENT WITH THE TWIN LAW K,H,-L AND A REFINED TWIN FRACTION OF 0.35. 5. THE R-FREE SET WAS GENERATED WITH THE TWIN LAW. 6. REFINEMENT WAS AGAINST INTENSITY DATA.
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Displacement parameters | Biso mean: 19.798 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 2887 / Occupancy sum non hydrogen: 3307.5 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→27.84 Å
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Refine LS restraints |
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