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- PDB-7evq: Crystal structure of C-terminal half of lactoferrin obtained by l... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7evq | ||||||
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Title | Crystal structure of C-terminal half of lactoferrin obtained by limited proteolysis using pepsin at 2.6 A resolution | ||||||
![]() | Lactotransferrin | ||||||
![]() | IRON-BINDING PROTEIN / lactoferrin | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Viswanathan, V. / Singh, J. / Sharma, P. / Sharma, S. / Singh, T.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of C-terminal half of lactoferrin obtained by limited proteolysis using pepsin at 2.6 A resolution Authors: Viswanathan, V. / Singh, J. / Sharma, P. / Sharma, S. / Singh, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.9 KB | Display | ![]() |
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PDB format | ![]() | 120.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Data in CIF | ![]() | 40.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bfl S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.192071926117, -0.0369469481605, -0.980685116752), (-0.0425013599465, 0.998040348997, -0.0459248971302), (0.980460100973, 0.0505013345897, 0.190125236631)Vector: 75. ...NCS oper: (Code: given Matrix: (0.192071926117, -0.0369469481605, -0.980685116752), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38011.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P24627, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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-Sugars , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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 #5: Sugar | |
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-Non-polymers , 4 types, 86 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Magnesium Acetate 20%, PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9655 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45.12 Å / Num. obs: 41125 / % possible obs: 64.8 % / Redundancy: 3 % / Biso Wilson estimate: 43.83 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.039 / Rrim(I) all: 0.078 / Net I/σ(I): 0.97 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1136 / CC1/2: 0.84 / Rpim(I) all: 0.26 / Rrim(I) all: 0.48 / % possible all: 22.2 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1BFL ![]() 1bfl Resolution: 2.6→45.12 Å / SU ML: 0.4187 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.9683 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→45.12 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.1512745831 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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