+Open data
-Basic information
Entry | Database: PDB / ID: 1h44 | ||||||
---|---|---|---|---|---|---|---|
Title | R210L N-TERMINAL LOBE HUMAN LACTOFERRIN | ||||||
Components | LACTOFERRIN | ||||||
Keywords | METAL TRANSPORT / IRON TRANSPORT / METAL BINDING | ||||||
Function / homology | Function and homology information 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 / negative regulation of osteoclast development / specific granule / 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 / ossification / regulation of cytokine production / protein serine/threonine kinase activator activity / 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 / positive regulation of canonical NF-kappaB signal transduction / iron ion transport / antibacterial humoral response / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Peterson, N.A. / Arcus, V.L. / Anderson, B.F. / Jameson, G.B. / Tweedie, J.W. / Baker, E.N. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: "Dilysine Trigger" in Transferrins Probed by Mutagenesis of Lactoferrin: Crystal Structures of the R210G, R210E, and R210L Mutants of Human Lactoferrin Authors: Peterson, N.A. / Arcus, V.L. / Anderson, B.F. / Tweedie, J.W. / Jameson, G.B. / Baker, E.N. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1h44.cif.gz | 83 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1h44.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1h44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h44_validation.pdf.gz | 378.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1h44_full_validation.pdf.gz | 382.9 KB | Display | |
Data in XML | 1h44_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1h44_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/1h44 ftp://data.pdbj.org/pub/pdb/validation_reports/h4/1h44 | HTTPS FTP |
-Related structure data
Related structure data | 1h43C 1h45C 1lctS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37106.176 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LOBE, RESIDUES 20-353 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): BHK / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P02788 |
---|---|
#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-CO3 / |
#4: Water | ChemComp-HOH / |
Compound details | IRON BINDING TRANSPORT PROTEINS THAT CAN BIND TWO FERRIC IRONS IN ASSOCIATION WITH THE BINDING OF ...IRON BINDING TRANSPORT PROTEINS THAT CAN BIND TWO FERRIC IRONS IN ASSOCIATIO |
Sequence details | IN RELATED PDB ID 1H43, THERE IS A SEQUENCE MISMATCH AT RESIDUE 28, THE SEQUENCE THAT WAS USED IN ...IN RELATED PDB ID 1H43, THERE IS A SEQUENCE MISMATCH AT RESIDUE 28, THE SEQUENCE THAT WAS USED IN THIS WORK IS FROM THE SEQUENCING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.05 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8 / Details: HEPES, NACL, pH 8.00 | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: batch method | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 113 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
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: 2→30 Å / Num. obs: 23271 / % possible obs: 94.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.5 / % possible all: 89 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / Redundancy: 2.8 % |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 89 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LCT Resolution: 2→31.23 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.3959 Å2 / ksol: 0.377997 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→31.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 32 Å / Num. reflection obs: 23270 / Num. reflection Rfree: 2179 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|