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Yorodumi- PDB-4r4g: Crystal structure of a putative lipoprotein (ycdA) from Bacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r4g | ||||||
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Title | Crystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution | ||||||
Components | putative lipoprotein YcdA | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two domain protein / N-terminal domain has Ig-like fold / belongs to DUF4352 family (PF11611) / C-terminal domain has fold: alpha(2)-beta(2)-alpha(2)-beta-alpha / domains connected by kinked-helix / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Domain of unknown function DUF5105 / Domain of unknown function (DUF5105) / Domain of unknown function DUF4352 / Domain of unknown function (DUF4352) / Immunoprotective extracellular, immunoglobulin-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / Uncharacterized lipoprotein YcdA Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.62 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r4g.cif.gz | 140.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r4g.ent.gz | 114.8 KB | Display | PDB format |
PDBx/mmJSON format | 4r4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r4g_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 4r4g_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 4r4g_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 4r4g_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/4r4g ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r4g | 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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Unit cell |
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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 36286.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: ycdA, BSU02780 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: O34538 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (30-354) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (30-354) WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 50.0% polyethylene glycol 200, 0.1M TRIS pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97971,0.91837,0.97926 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2014 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.62→49.327 Å / Num. obs: 17632 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 84.781 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.88 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.023 / Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.62→49.327 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.9075 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. PEG (PG4) MODELED WERE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
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Displacement parameters | Biso max: 166.83 Å2 / Biso mean: 89.4081 Å2 / Biso min: 49.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.506 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→49.327 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.62→2.78 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 1.5638 Å / Origin y: 39.7534 Å / Origin z: 86.9264 Å
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Refinement TLS group | Selection details: {A|33 - 354} |