+Open data
-Basic information
Entry | Database: PDB / ID: 6gqz | ||||||
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Title | Petrobactin-binding engineered lipocalin without ligand | ||||||
Components | Neutrophil gelatinase-associated lipocalin | ||||||
Keywords | TRANSPORT PROTEIN / ANTICALIN / BETA-BARREL / PETROBACTIN / LCN2 / LIPOCALIN / NGAL / PROTEIN ENGINEERING | ||||||
Function / homology | Function and homology information siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / small molecule binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium ...siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / small molecule binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium / iron ion binding / innate immune response / apoptotic process / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Skerra, A. / Eichinger, A. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: Reprogramming Human Siderocalin To Neutralize Petrobactin, the Essential Iron Scavenger of Anthrax Bacillus. Authors: Dauner, M. / Eichinger, A. / Lucking, G. / Scherer, S. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gqz.cif.gz | 173.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gqz.ent.gz | 136.8 KB | Display | PDB format |
PDBx/mmJSON format | 6gqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/6gqz ftp://data.pdbj.org/pub/pdb/validation_reports/gq/6gqz | HTTPS FTP |
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-Related structure data
Related structure data | 6gr0C 4mviS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 5 - 178 / Label seq-ID: 1 - 174
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-Components
#1: Protein | Mass: 20133.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Production host: Escherichia coli (E. coli) / References: UniProt: P80188 #2: Water | ChemComp-HOH / | |
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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: 2.15 Å3/Da / Density % sol: 42.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 1.8 M ammonium sulfate, 0.1 M bicine/NaOH |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 31, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.181→67.466 Å / Num. obs: 64603 / % possible obs: 96.3 % / Redundancy: 6.1 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Rsym value: 0.066 / Net I/av σ(I): 4.9 / Net I/σ(I): 13.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MVI Resolution: 1.4→33.41 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.209 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0638 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.061 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.72 Å2 / Biso mean: 18.003 Å2 / Biso min: 6.89 Å2
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Refinement step | Cycle: final / Resolution: 1.4→33.41 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 5577 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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