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Yorodumi- PDB-1zma: Crystal Structure of the Bacterocin Transport Accessory Protein f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zma | ||||||
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Title | Crystal Structure of the Bacterocin Transport Accessory Protein from Streptococcus pneumoniae | ||||||
Components | bacterocin transport accessory protein | ||||||
Keywords | TRANSPORT PROTEIN / alpha-beta-alpha-sandwich / bacterocin transport / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Bacteriocin transport accessory protein / bacteriocin biosynthetic process / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / Bacterocin transport accessory protein Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å | ||||||
Authors | Kim, Y. / Hatzos, C. / Abdullah, J. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The Crystal Structure of the Bacterocin Transport Accessory Protein from Streptococcus pneumoniae Authors: Kim, Y. / Hatzos, C. / Abdullah, J. / Collart, 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 | 1zma.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zma.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zma_validation.pdf.gz | 431.3 KB | Display | wwPDB validaton report |
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Full document | 1zma_full_validation.pdf.gz | 432.7 KB | Display | |
Data in XML | 1zma_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 1zma_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/1zma ftp://data.pdbj.org/pub/pdb/validation_reports/zm/1zma | 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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-Components
#1: Protein | Mass: 13247.632 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q8DP51 |
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#2: Chemical | ChemComp-FMT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 3350, HEPES, Sodium Chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Apr 8, 2005 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→25.5 Å / Num. all: 25134 / Num. obs: 24991 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 6.8 / % possible all: 51.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.25→25.5 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.533 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS FOR THE REFINEMENT.
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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: 9.835 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→25.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.253→1.286 Å / Total num. of bins used: 20
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