+Open data
-Basic information
Entry | Database: PDB / ID: 6tlb | ||||||
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Title | Plasmodium falciparum lipocalin (PF3D7_0925900) | ||||||
Components | Serine/threonine protein kinase | ||||||
Keywords | UNKNOWN FUNCTION / Lipocalin / Malaria / Infection | ||||||
Function / homology | Calycin / Parasitophorous vacuolar protein 5, putative Function and homology information | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SOLUTION SCATTERING / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Burda, P.C. / Crosskey, T.D. / Lauk, K. / Wilmanns, M. / Gilberger, T.W. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Cell Rep / Year: 2020 Title: Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum. Authors: Burda, P.C. / Crosskey, T. / Lauk, K. / Zurborg, A. / Sohnchen, C. / Liffner, B. / Wilcke, L. / Pietsch, E. / Strauss, J. / Jeffries, C.M. / Svergun, D.I. / Wilson, D.W. / Wilmanns, M. / Gilberger, T.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tlb.cif.gz | 158.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tlb.ent.gz | 126.1 KB | Display | PDB format |
PDBx/mmJSON format | 6tlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tlb_validation.pdf.gz | 466.2 KB | Display | wwPDB validaton report |
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Full document | 6tlb_full_validation.pdf.gz | 473.2 KB | Display | |
Data in XML | 6tlb_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 6tlb_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/6tlb ftp://data.pdbj.org/pub/pdb/validation_reports/tl/6tlb | HTTPS FTP |
-Related structure data
Related structure data | 3mbtS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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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: 22241.195 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: PF3D7_0925900 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I2Q0 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.76 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7 Details: 0.2 M magnesium chloride, 0.1 M Tris pH7, 2.5 M Sodium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→56.2 Å / Num. obs: 28936 / % possible obs: 99.75 % / Redundancy: 2 % / Biso Wilson estimate: 54.95 Å2 / CC1/2: 0.546 / Rmerge(I) obs: 0.1985 / Rrim(I) all: 0.2943 / Net I/σ(I): 3.69 |
Reflection shell | Resolution: 2.85→2.952 Å / Mean I/σ(I) obs: 1.19 / Num. unique obs: 2889 / CC1/2: 0.41 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MBT Resolution: 2.85→56.2 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.431 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 0.734 / ESU R Free: 0.321 / 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: 53.494 Å2
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Refinement step | Cycle: 1 / Resolution: 2.85→56.2 Å
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Refine LS restraints |
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