+Open data
-Basic information
Entry | Database: PDB / ID: 3h0t | ||||||
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Title | Hepcidin-Fab complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM/Antimicrobial Protein / Peptide-Fab complex / Antibiotic / Antimicrobial / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Fungicide / Hormone / Secreted / IMMUNE SYSTEM-Antimicrobial Protein COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of intestinal absorption / iron ion transmembrane transport / macrophage activation / positive regulation of macrophage activation / response to iron ion / negative regulation of bone resorption / negative regulation of iron ion transmembrane transport / myeloid cell homeostasis / cell surface receptor signaling pathway via JAK-STAT / defense response to fungus ...negative regulation of intestinal absorption / iron ion transmembrane transport / macrophage activation / positive regulation of macrophage activation / response to iron ion / negative regulation of bone resorption / negative regulation of iron ion transmembrane transport / myeloid cell homeostasis / cell surface receptor signaling pathway via JAK-STAT / defense response to fungus / establishment of localization in cell / protein catabolic process / hormone activity / multicellular organismal-level iron ion homeostasis / negative regulation of inflammatory response / positive regulation of protein catabolic process / intracellular iron ion homeostasis / killing of cells of another organism / transcription by RNA polymerase II / defense response to bacterium / inflammatory response / immune response / copper ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Syed, R. / Li, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Hepcidin revisited, disulfide connectivity, dynamics, and structure. Authors: Jordan, J.B. / Poppe, L. / Haniu, M. / Arvedson, T. / Syed, R. / Li, V. / Kohno, H. / Kim, H. / Schnier, P.D. / Harvey, T.S. / Miranda, L.P. / Cheetham, J. / Sasu, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h0t.cif.gz | 109.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h0t.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 3h0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h0t_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
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Full document | 3h0t_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 3h0t_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 3h0t_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/3h0t ftp://data.pdbj.org/pub/pdb/validation_reports/h0/3h0t | HTTPS FTP |
-Related structure data
Related structure data | 2kefC 8fabS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 23132.346 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 25501.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#3: Protein/peptide | Mass: 2802.455 Da / Num. of mol.: 1 / Fragment: UNP residues 60-84 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HAMP, HEPC, hepcidin, LEAP1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P81172 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES,70% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→86.07 Å / Num. obs: 41776 / % possible obs: 94 % / Observed criterion σ(F): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 25.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 8FAB Resolution: 1.89→86.07 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.076 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.151 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.371 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→86.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.944 Å / Total num. of bins used: 20
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