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Yorodumi- PDB-2ywm: Crystal structure of glutaredoxin-like protein from Aquifex aeolicus -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ywm | ||||||
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Title | Crystal structure of glutaredoxin-like protein from Aquifex aeolicus | ||||||
Components | Glutaredoxin-like protein | ||||||
Keywords | OXIDOREDUCTASE / Redox protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Glutaredoxin-like, bacteria/archaea / Thioredoxin domain / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Glutaredoxin-like protein Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of glutaredoxin-like protein from Aquifex aeolicus Authors: Ebihara, A. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ywm.cif.gz | 181.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ywm.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ywm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ywm_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 2ywm_full_validation.pdf.gz | 452.2 KB | Display | |
Data in XML | 2ywm_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 2ywm_validation.cif.gz | 47 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/2ywm ftp://data.pdbj.org/pub/pdb/validation_reports/yw/2ywm | 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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-Components
#1: Protein | Mass: 25853.059 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: O66753 #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: 4.61 Å3/Da / Density % sol: 73.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.9M Ammonium phosphate, 90MM Sodium acetate, 90MM Lithium sulfate, 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: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9789, 0.9000, 0.9794 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: May 16, 2006 | ||||||||||||
Radiation | Monochromator: SI Double-Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→50 Å / Num. obs: 83966 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 26.7 | ||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 5.11 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2119859.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.1153 Å2 / ksol: 0.362188 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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