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Yorodumi- PDB-3ib2: structure of the complex of C-terminal half (C-lobe) of bovine la... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ib2 | ||||||||||||
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Title | structure of the complex of C-terminal half (C-lobe) of bovine lactoferrin with alpha-methyl-4-(2-methylpropyl) benzene acetic acid | ||||||||||||
Components | Lactotransferrin | ||||||||||||
Keywords | METAL BINDING PROTEIN / COMPLEX / IBUPROFEN / C-LOBE / Antibiotic / Antimicrobial / Disulfide bond / Glycoprotein / Hydrolase / Ion transport / Iron / Iron transport / Metal-binding / Phosphoprotein / Protease / Secreted / Serine protease / Transport | ||||||||||||
Function / homology | Function and homology information Metal sequestration by antimicrobial proteins / Antimicrobial peptides / 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 ...Metal sequestration by antimicrobial proteins / Antimicrobial peptides / 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 / regulation of tumor necrosis factor production / bone morphogenesis / Neutrophil degranulation / cysteine-type endopeptidase inhibitor activity / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / innate immune response in mucosa / recycling endosome / iron ion transport / antibacterial humoral response / early endosome / iron ion binding / serine-type endopeptidase activity / signaling receptor binding / negative regulation of apoptotic process / proteolysis / extracellular space / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||||||||
Authors | Mir, R. / Vikram, G. / Kumar, R.P. / Sinha, M. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P. | ||||||||||||
Citation | Journal: Biophys.J. / Year: 2009 Title: The structural basis for the prevention of nonsteroidal antiinflammatory drug-induced gastrointestinal tract damage by the C-lobe of bovine colostrum lactoferrin. Authors: Mir, R. / Singh, N. / Vikram, G. / Kumar, R.P. / Sinha, M. / Bhushan, A. / Kaur, P. / Srinivasan, A. / Sharma, S. / 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 | 3ib2.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ib2.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ib2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ib2_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3ib2_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3ib2_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 3ib2_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/3ib2 ftp://data.pdbj.org/pub/pdb/validation_reports/ib/3ib2 | HTTPS FTP |
-Related structure data
Related structure data | 3iazC 3ib0C 3ib1C 2dwaS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37655.504 Da / Num. of mol.: 1 / Fragment: UNP residues 361-705 / Mutation: N565K, K608E / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P24627, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Non-polymers , 6 types, 146 molecules
#4: Chemical | ChemComp-IBP / | ||||
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#5: Chemical | ChemComp-FE / | ||||
#6: Chemical | ChemComp-CO3 / | ||||
#7: Chemical | #8: Chemical | ChemComp-SO4 / | #9: Water | ChemComp-HOH / | |
-Details
Sequence details | THERE ARE CONFLICTS BETWEEN SEQRES (LYS A 565, GLU A 608) AND SEQUENCE DATABASE (ASN, LYS). THE ...THERE ARE CONFLICTS BETWEEN SEQRES (LYS A 565, GLU A 608) AND SEQUENCE DATABASE (ASN, LYS). THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THESE RESIDUES AND IS NATURAL MUTANT. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.01M ZNSO4, 0.1M MES, 25% PEG, MONOMETHYL ETHER 550, PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 18, 2007 / Details: MIRROR |
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: 2.29→20 Å / Num. obs: 15854 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.125 / Rsym value: 0.064 |
Reflection shell | Resolution: 2.29→2.38 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.477 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DWA Resolution: 2.29→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.88 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.364 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.35 Å / Total num. of bins used: 20
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