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Yorodumi- PDB-3k2g: Crystal structure of a Resiniferatoxin-binding protein from Rhodo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k2g | ||||||
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Title | Crystal structure of a Resiniferatoxin-binding protein from Rhodobacter sphaeroides | ||||||
Components | Resiniferatoxin-binding, phosphotriesterase-related protein | ||||||
Keywords | Resiniferatoxin binding protein / Resiniferatoxin-binding / phosphotriesterase / TIM BARREL / Binuclear Zinc / PROTEIN STRUCTURE INITIATIVE II (PSI II) / STRUCTURAL GENOMICS / NYSGXRC / 9588c / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information catabolic process / phosphoric diester hydrolase activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides 2.4.1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a Resiniferatoxin-binding protein from Rhodobacter sphaeroides Authors: Kumaran, D. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k2g.cif.gz | 296 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k2g.ent.gz | 251.2 KB | Display | PDB format |
PDBx/mmJSON format | 3k2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k2g_validation.pdf.gz | 480.4 KB | Display | wwPDB validaton report |
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Full document | 3k2g_full_validation.pdf.gz | 504.5 KB | Display | |
Data in XML | 3k2g_validation.xml.gz | 60.9 KB | Display | |
Data in CIF | 3k2g_validation.cif.gz | 87.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/3k2g ftp://data.pdbj.org/pub/pdb/validation_reports/k2/3k2g | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | Authors state that the biological unit is tetramer. |
-Components
#1: Protein | Mass: 40970.367 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria) Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RHOS4_37320, RHOS4_37320 (RSP_3690), RSP_3690 / Plasmid: BC-PSGX3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3IVY4 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-DTV / ( #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: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% PEG 3350, 0.2 M MgCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 127592 / Num. obs: 127592 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2 / Num. unique all: 7765 / % possible all: 55.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→44.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 121012.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.783 Å2 / ksol: 0.360686 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→44.79 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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