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Yorodumi- PDB-1fb6: CRYSTAL STRUCTURE OF THIOREDOXIN M FROM SPINACH CHLOROPLAST (OXID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fb6 | ||||||
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Title | CRYSTAL STRUCTURE OF THIOREDOXIN M FROM SPINACH CHLOROPLAST (OXIDIZED FORM) | ||||||
Components | THIOREDOXIN M | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information protein-disulfide reductase activity / enzyme activator activity / chloroplast Similarity search - Function | ||||||
Biological species | Spinacia oleracea (spinach) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Capitani, G. / Markovic-Housley, Z. / DelVal, G. / Morris, M. / Jansonius, J.N. / Schurmann, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structures of two functionally different thioredoxins in spinach chloroplasts. Authors: Capitani, G. / Markovic-Housley, Z. / DelVal, G. / Morris, M. / Jansonius, J.N. / Schurmann, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fb6.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fb6.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fb6_validation.pdf.gz | 419.3 KB | Display | wwPDB validaton report |
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Full document | 1fb6_full_validation.pdf.gz | 421.5 KB | Display | |
Data in XML | 1fb6_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1fb6_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/1fb6 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/1fb6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 11793.436 Da / Num. of mol.: 2 / Fragment: OXIDIZED FORM Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spinacia oleracea (spinach) / Cellular location: CHLOROPLAST / Plasmid: PKK233-2 (MODIFIED) / Production host: Escherichia coli (E. coli) / References: UniProt: P07591 #2: 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: 2.53 Å3/Da / Density % sol: 51.31 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: sodium acetate, PEG monomethylether 2000, ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.3 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 31, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.6 Å / Num. obs: 14256 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.396 / % possible all: 92 |
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Resolution: 2.1→29.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Used overall anisotropic B-factor refinement and bulk solvent correction (X-PLOR 3.851 and CNS)
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Refinement step | Cycle: LAST / Resolution: 2.1→29.6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 29.6 Å / σ(F): 0 / % reflection Rfree: 3.8 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.23 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.3 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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