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- PDB-1l5t: Crystal Structure of a Domain-Opened Mutant (R121D) of the Human ... -
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Basic information
Entry | Database: PDB / ID: 1l5t | ||||||
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Title | Crystal Structure of a Domain-Opened Mutant (R121D) of the Human Lactoferrin N-lobe Refined From a Merohedrally-Twinned Crystal Form. | ||||||
![]() | lactoferrin | ||||||
![]() | METAL TRANSPORT / IRON TRANSPORT / GLYCOPROTEIN / LACTOFERRIN / N-LOBE / IRON-RELEASE / TWINNING | ||||||
Function / homology | ![]() negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism ...negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of lipopolysaccharide-mediated signaling pathway / specific granule / negative regulation of osteoclast development / antifungal humoral response / positive regulation of chondrocyte proliferation / negative regulation of ATP-dependent activity / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / cysteine-type endopeptidase inhibitor activity / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / humoral immune response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / protein serine/threonine kinase activator activity / ossification / innate immune response in mucosa / secretory granule / lipopolysaccharide binding / positive regulation of protein serine/threonine kinase activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / positive regulation of NF-kappaB transcription factor activity / heparin binding / iron ion transport / antibacterial humoral response / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / killing of cells of another organism / early endosome / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jameson, G.B. / Anderson, B.F. / Breyer, W.A. / Tweedie, J.W. / Baker, E.N. | ||||||
![]() | ![]() Title: Structure of a domain-opened mutant (R121D) of the human lactoferrin N-lobe refined from a merohedrally twinned crystal form. Authors: Jameson, G.B. / Anderson, B.F. / Breyer, W.A. / Day, C.L. / Tweedie, J.W. / Baker, E.N. #1: ![]() Title: On the Molecular-Replacement Problem in the Presence of Merohedral Twinning: Structure of the N-Terminal Half-Molecule of Human Lactoferrin Authors: Breyer, W.A. / Kingston, R.L. / Anderson, B.F. / Baker, E.N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.3 KB | Display | ![]() |
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PDB format | ![]() | 108.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.5 KB | Display | ![]() |
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Full document | ![]() | 462.4 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lctS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36921.875 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-352 / Mutation: R121D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.35 Å3/Da / Density % sol: 71.7 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 8 Details: concentrated solution of the protein (50-80 mg mL-1), 0.01 M Tris-HCl, pH 8.0, 12% (v/v) isopropanol, MICRODIALYSIS, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1994 / Details: graphite monochromator |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 23431 / % possible obs: 96 % / Observed criterion σ(F): 4 / Redundancy: 2.8 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.418 / % possible all: 93 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 23882 / % possible obs: 96 % |
Reflection shell | *PLUS Highest resolution: 3 Å / % possible obs: 93 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1lct Resolution: 3→10 Å / Num. parameters: 19883 / Num. restraintsaints: 27798 Isotropic thermal model: INDIVIDUAL, WITH TIGHT ADJACENCY AND NCS RESTRAINTS, AND IDENTITY CONSTRAINTS ON NEARLY CHEMICALLY EQUIVALENT REDIDUES (E.G. OE1 AND OE2 OF GLU) Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: WEIGHTED CONJUGATE-GRADIENT REFINEMENT ON F-SQUARED; HEMIHEDRAL TWINNING TO GIVE PSEUDO-HEXAGONAL (6/M) DIFFRACTION SYMMETRY; TWIN RATIO=0.44035:0.54965. WITH REGARDS TO THE TORSION ANGLES ...Details: WEIGHTED CONJUGATE-GRADIENT REFINEMENT ON F-SQUARED; HEMIHEDRAL TWINNING TO GIVE PSEUDO-HEXAGONAL (6/M) DIFFRACTION SYMMETRY; TWIN RATIO=0.44035:0.54965. WITH REGARDS TO THE TORSION ANGLES OF LEU 299, THE RESIDUE IS PART OF A CONSERVED GAMMA TURN.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, 1975 K(SOLV)=0.551302, B(SOLV)=2.7660 Bsol: 2.766 Å2 / ksol: 0.551302 e/Å3 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5241 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. reflection obs: 22636 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |