+Open data
-Basic information
Entry | Database: PDB / ID: 1biy | ||||||
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Title | STRUCTURE OF DIFERRIC BUFFALO LACTOFERRIN | ||||||
Components | LACTOFERRIN | ||||||
Keywords | IRON-BINDING PROTEIN / IRON BINDING PROTEIN / LACTOFERRIN / ANTIBACTERIAL | ||||||
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 / ossification / regulation of cytokine production / innate immune response in mucosa / recycling endosome / iron ion transport / antibacterial humoral response / early endosome / iron ion binding / serine-type endopeptidase activity / negative regulation of apoptotic process / proteolysis / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Bubalus bubalis (water buffalo) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.37 Å | ||||||
Authors | Karthikeyan, S. / Yadav, S. / Singh, T.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structure of buffalo lactoferrin at 3.3 A resolution at 277 K. Authors: Karthikeyan, S. / Yadav, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P. #1: Journal: J.Mol.Biol. / Year: 1997 Title: Three-Dimensional Structure of Diferric Bovine Lactoferrin at 2.8 A Resolution Authors: Moore, S.A. / Anderson, B.F. / Groom, C.R. / Haridas, M. / Baker, E.N. #2: Journal: Arch.Biochem.Biophys. / Year: 1992 Title: Purification, Crystallization, and X-Ray Diffraction Studies of Lactotransferrin from Buffalo Colostrum Authors: Raman, A. / Bhatia, K.L. / Singh, T.P. / Srinivasan, A. / Betzel, C. / Malik, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1biy.cif.gz | 130.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1biy.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 1biy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1biy_validation.pdf.gz | 384.9 KB | Display | wwPDB validaton report |
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Full document | 1biy_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 1biy_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 1biy_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/1biy ftp://data.pdbj.org/pub/pdb/validation_reports/bi/1biy | 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: 75862.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bubalus bubalis (water buffalo) / Cellular location: EXTRACELLULAR / Secretion: MILK / References: UniProt: O77698 | ||
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#2: Chemical | #3: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.3 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: microdialysis | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: PINHOLE |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.37→17 Å / Num. obs: 11711 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 3.68 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.0507 / Rsym value: 0.0507 / Net I/σ(I): 34.47 |
Reflection shell | Resolution: 3.37→3.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 13.35 / Rsym value: 0.135 / % possible all: 97.6 |
Reflection | *PLUS Highest resolution: 3.3 Å / % possible obs: 98.5 % / Num. measured all: 42104 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS Highest resolution: 3.3 Å / Lowest resolution: 3.5 Å / % possible obs: 60 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 5.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HUMAN DIFERRIC LACTOFERRIN Resolution: 3.37→17 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: A POSTERIORI / σ(F): 0
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Displacement parameters | Biso mean: 32.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 17 Å / Luzzati sigma a obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.37→17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.37→3.58 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 11711 / Rfactor Rfree: 0.296 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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