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Yorodumi- PDB-4jg9: X-ray Crystal Structure of a Putative Lipoprotein from Bacillus a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jg9 | ||||||
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Title | X-ray Crystal Structure of a Putative Lipoprotein from Bacillus anthracis | ||||||
Components | Lipoprotein | ||||||
Keywords | LIPID BINDING PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Immunoglobulin-like - #3830 / Protein of unknown function DUF4871 / Domain of unknown function (DUF4871) / Immunoglobulin-like / Sandwich / Mainly Beta / DUF4871 domain-containing protein / Putative lipoprotein Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.425 Å | ||||||
Authors | Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: X-ray Crystal Structure of a Putative Lipoprotein from Bacillus anthracis Authors: Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jg9.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jg9.ent.gz | 100.7 KB | Display | PDB format |
PDBx/mmJSON format | 4jg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jg9_validation.pdf.gz | 428.5 KB | Display | wwPDB validaton report |
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Full document | 4jg9_full_validation.pdf.gz | 430.7 KB | Display | |
Data in XML | 4jg9_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 4jg9_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/4jg9 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/4jg9 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19754.713 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_0580, BAS0549, GBAA_0580 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q81VB7, UniProt: A0A6L7HR41*PLUS #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: 3.18 Å3/Da / Density % sol: 61.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.4M Na Citrate, 0.1M HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2012 / Details: Be Lens |
Radiation | Monochromator: Single Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.425→70.925 Å / Num. all: 20467 / Num. obs: 20467 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.425→2.57 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3209 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.425→70.925 Å / SU ML: 0.23 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.11 / Phase error: 20.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.425→70.925 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 26.7802 Å / Origin y: 41.4265 Å / Origin z: 128.9542 Å
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Refinement TLS group | Selection details: all |