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Yorodumi- PDB-1qjm: Crystal Structure of a Complex of Lactoferrin with a Lanthanide I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qjm | ||||||
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Title | Crystal Structure of a Complex of Lactoferrin with a Lanthanide Ion (SM3+) at 3.4 Angstrom Resolution | ||||||
Components | LACTOFERRIN | ||||||
Keywords | LACTOFERRIN / COMPLEX / IRON BINDING / TRANSFERRIN | ||||||
Function / homology | Function and homology information 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 / regulation of tumor necrosis factor production / bone morphogenesis ...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 / regulation of tumor necrosis factor production / bone morphogenesis / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / serine-type peptidase activity / ossification / innate immune response in mucosa / recycling endosome / antibacterial humoral response / iron ion transport / early endosome / negative regulation of apoptotic process / proteolysis / extracellular space / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | EQUUS CABALLUS (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Sharma, A.K. / Singh, T.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Lactoferrin-Metal Interactions: First Crystal Structure of a Complex of Lactoferrin with a Lanthanide Ion (Sm3+) at 3.4 Angstrom Resolution Authors: Sharma, A.K. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qjm.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qjm.ent.gz | 96 KB | Display | PDB format |
PDBx/mmJSON format | 1qjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/1qjm ftp://data.pdbj.org/pub/pdb/validation_reports/qj/1qjm | HTTPS FTP |
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-Related structure data
Related structure data | 1bgr S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 75371.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) EQUUS CABALLUS (horse) / Secretion: MILK / References: UniProt: O77811 | ||||
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#2: Chemical | #3: Chemical | Sequence details | THE SEQUENCE WAS DETERMINED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 8 Details: PROTEIN SOLUTION WITH A CONCENTRATION OF 40MG/ML IN 0.025M TRIS-HCL WAS EQUILIBRATED AGAINST THE SAME BUFFER CONTAINING 10% (V/V) ETHANOL AT PH 8.0 AT 4 DEGREE. | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: microdialysis | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998 / Details: PINHOLE |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→17 Å / Num. obs: 8782 / % possible obs: 85 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.126 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 3.4→3.8 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.263 / % possible all: 55 |
Reflection | *PLUS Num. measured all: 75612 / Rmerge(I) obs: 0.126 |
Reflection shell | *PLUS % possible obs: 55 % / Rmerge(I) obs: 0.263 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BGR 1bgr Resolution: 3.4→17 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3.4→17 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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