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Open data
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Basic information
Entry | Database: PDB / ID: 2j4u | ||||||
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Title | E.coli OmpC - camel Lactoferrin complex | ||||||
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![]() | MEMBRANE PROTEIN/HYDROLASE / MEMBRANE PROTEIN-HYDROLASE COMPLEX / IRON / OMPC / PORIN / COMPLEX / PROTEASE / HYDROLASE / MEMBRANE PROTEIN / ANTIACTERIAL PEPTIDE / ION TRANSPORT / IRON TRANSPORT / SERINE PROTEASE / TRANSPORT / LACTOFERRIN / GLYCOPROTEIN / METAL-BINDING | ||||||
Function / homology | ![]() 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 / porin activity / pore complex / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / monoatomic ion transmembrane transport / regulation of cytokine production / ossification / innate immune response in mucosa / cell outer membrane / recycling endosome / virus receptor activity / iron ion transport / antibacterial humoral response / receptor-mediated virion attachment to host cell / early endosome / iron ion binding / serine-type endopeptidase activity / DNA damage response / negative regulation of apoptotic process / proteolysis / extracellular space / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Baalaji, S. / Acharya, R.K. / Singh, T.P. / Krishnaswamy, S. | ||||||
![]() | ![]() Title: Crystal Structure of the Membrane Protein Ompc Complex with Antibacterial Lactoferrin Authors: Baalaji, S. / Acharya, R.K. / Singh, T.P. / Krishnaswamy, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 17-STRANDED BARREL THIS IS REPRESENTED BY A 18-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "UA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "VA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "WA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 417.8 KB | Display | ![]() |
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PDB format | ![]() | 331.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 515.8 KB | Display | ![]() |
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Full document | ![]() | 853.4 KB | Display | |
Data in XML | ![]() | 114.9 KB | Display | |
Data in CIF | ![]() | 147.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 38336.242 Da / Num. of mol.: 6 / Fragment: RESIDUES 22-367 / Source method: isolated from a natural source / Details: LAB COLLECTION / Source: (natural) ![]() ![]() #2: Protein/peptide | Mass: 5203.188 Da / Num. of mol.: 2 / Fragment: N-TERM FRAGMENT, RESIDUES 20-64 / Source method: isolated from a natural source Details: ONLY 45 RESIDUES SEEN REMAINING COULD NOT BE LOCATED DUE TO DISORDER. Source: (natural) ![]() ![]() References: UniProt: Q9TUM0, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases Sequence details | SIGNAL PEPTIDE NOT PRESENT ONLY THE FIRST 45 RESIDUES ARE SEEN. THE REST COULD NOT BE LOCATED DUE TO DISORDER | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 59.7 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 5, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 55942 / % possible obs: 79 % / Observed criterion σ(I): 1 / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.4 / % possible all: 73 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1OSM, 1DTZ Resolution: 2.99→152.5 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.857 / SU B: 15.655 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.99→152.5 Å
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