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Yorodumi- PDB-1b7u: Structure of Mare Apolactoferrin: the N and C Lobes are in the Cl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b7u | ||||||
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Title | Structure of Mare Apolactoferrin: the N and C Lobes are in the Closed Form | ||||||
Components | Lactotransferrin | ||||||
Keywords | METAL BINDING PROTEIN / APOLACTOFERRIN / BINDING SITE | ||||||
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 / negative regulation of osteoclast development / specific granule / 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 / negative regulation of osteoclast development / specific granule / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Sharma, A.K. / Singh, T.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structure of mare apolactoferrin: the N and C lobes are in the closed form. Authors: Sharma, A.K. / Rajashankar, K.R. / Yadav, M.P. / 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 | 1b7u.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b7u.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 1b7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b7u_validation.pdf.gz | 373.3 KB | Display | wwPDB validaton report |
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Full document | 1b7u_full_validation.pdf.gz | 463.3 KB | Display | |
Data in XML | 1b7u_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 1b7u_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/1b7u ftp://data.pdbj.org/pub/pdb/validation_reports/b7/1b7u | 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: 75371.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Secretion: MILK References: UniProt: O77811, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 51 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 / Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 277 K / Method: microdialysis | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8345 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→32 Å / Num. obs: 7887 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.15 / Rsym value: 0.15 / Net I/σ(I): 14 |
Reflection | *PLUS Num. measured all: 101096 |
Reflection shell | *PLUS Highest resolution: 3.8 Å / Lowest resolution: 4.09 Å / % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DIFERRIC MARE LACTOFERRIN Resolution: 3.8→32 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: POSTERIORI / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3.8→32 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 44.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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