+Open data
-Basic information
Entry | Database: PDB / ID: 3bws | ||||||
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Title | Crystal structure of the leptospiral antigen Lp49 | ||||||
Components | protein Lp49 | ||||||
Keywords | UNKNOWN FUNCTION / Two-domain / immunoglobulin-like / 7-bladed beta propeller | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Leptospira interrogans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å | ||||||
Authors | Giuseppe, P.O. / Neves, F.O. / Nascimento, A.L.T.O. / Guimaraes, B.G. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2008 Title: The leptospiral antigen Lp49 is a two-domain protein with putative protein binding function Authors: Giuseppe, P.O. / Neves, F.O. / Nascimento, A.L.T.O. / Guimaraes, B.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bws.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bws.ent.gz | 149.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bws_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 3bws_full_validation.pdf.gz | 452.1 KB | Display | |
Data in XML | 3bws_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 3bws_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/3bws ftp://data.pdbj.org/pub/pdb/validation_reports/bw/3bws | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 49592.988 Da / Num. of mol.: 2 / Fragment: Lp49 without predicted signal peptide Source method: isolated from a genetically manipulated source Details: expression vector encodes a N-terminal Histag / Source: (gene. exp.) Leptospira interrogans (bacteria) / Strain: Copenhageni, Fiocruz L1-130 isolate / Gene: LIC10793 / Plasmid: pAE / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q8F0X1, UniProt: Q72U69*PLUS #2: Chemical | #3: 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: 2.29 Å3/Da / Density % sol: 46.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8.5 Details: 0.2 M LiSO4, 15 % PEG 4000, 0.1 M Tris-HCl, microseeding, pH 8.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2007 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→53.45 Å / Num. obs: 60735 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 15.649 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.99→2.1 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 5.3 / Num. unique all: 8497 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.021 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.171 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.839 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.041 Å / Total num. of bins used: 20
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