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Yorodumi- PDB-3lno: Crystal Structure of Domain of Unknown Function DUF59 from Bacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lno | ||||||
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Title | Crystal Structure of Domain of Unknown Function DUF59 from Bacillus anthracis | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / alpha-beta fold / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Fe-S cluster assembly (FSCA) / MIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / DUF59 domain-containing protein / FeS_assembly_P domain-containing protein Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Kim, Y. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Domain of Unknown Function DUF59 Bacillus anthracis Authors: Kim, Y. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lno.cif.gz | 262.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lno.ent.gz | 225 KB | Display | PDB format |
PDBx/mmJSON format | 3lno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lno_validation.pdf.gz | 462.8 KB | Display | wwPDB validaton report |
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Full document | 3lno_full_validation.pdf.gz | 467.8 KB | Display | |
Data in XML | 3lno_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 3lno_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/3lno ftp://data.pdbj.org/pub/pdb/validation_reports/ln/3lno | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12127.860 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BAS4906, BA_5281, GBAA5281, GBAA_5281 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81XF6, UniProt: A0A6L8PPP9*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: 2.66 Å3/Da / Density % sol: 53.84 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M Acetate, 20% (v/v) 1,4-butanediol, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2009 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.94 Å / Num. all: 42911 / Num. obs: 42911 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.114 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 2084 / Rsym value: 0.484 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→45.94 Å / SU ML: 0.26 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.635 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→45.94 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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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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