+Open data
-Basic information
Entry | Database: PDB / ID: 1nm3 | ||||||
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Title | Crystal structure of Heamophilus influenza hybrid-Prx5 | ||||||
Components | Protein HI0572 | ||||||
Keywords | ELECTRON TRANSPORT / hybrid / peroxiredoxin / glutaredoxin | ||||||
Function / homology | Function and homology information glutathione-dependent peroxiredoxin / thioredoxin peroxidase activity / protein-disulfide reductase activity / cell redox homeostasis / hydrogen peroxide catabolic process / cellular response to oxidative stress / electron transfer activity / cytoplasm Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Kim, S.J. / Woo, J.R. / Hwang, Y.S. / Jeong, D.G. / Shin, D.H. / Kim, K.H. / Ryu, S.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The Tetrameric Structure of Haemophilus influenza Hybrid Prx5 Reveals Interactions between Electron Donor and Acceptor Proteins. Authors: Kim, S.J. / Woo, J.R. / Hwang, Y.S. / Jeong, D.G. / Shin, D.H. / Kim, K. / Ryu, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nm3.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nm3.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 1nm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nm3_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
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Full document | 1nm3_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 1nm3_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 1nm3_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/1nm3 ftp://data.pdbj.org/pub/pdb/validation_reports/nm/1nm3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27149.689 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / References: UniProt: P44758 #2: Chemical | ChemComp-SO4 / |
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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: 2.91 Å3/Da / Density % sol: 57.44 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium sulfate, sodium acetate, tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 22, 2001 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→99 Å / Num. all: 6059 / Num. obs: 15821 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.8→99 Å / % possible all: 98.5 |
Reflection | *PLUS Num. obs: 15906 / Num. measured all: 407938 / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.95 Å / % possible obs: 100 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→99 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→99 Å
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Refinement | *PLUS Lowest resolution: 99 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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