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Yorodumi- PDB-3b4q: Crystal structure of a conserved protein domain (unknown function... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b4q | ||||||
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Title | Crystal structure of a conserved protein domain (unknown function) from Corynebacterium diphtheriae | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC90667.1 / conserved protein domain / Corynebacterium diphtheriae / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information conserved protein domain from corynebacterium diphtheriae / Resuscitation-promoting factor Rpf1, C-terminal / Resuscitation-promoting factor Rpf1, C-terminal / Resuscitation-promoting factor, core lysozyme-like domain / Transglycosylase-like domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Corynebacterium diphtheriae NCTC 13129 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å | ||||||
Authors | Tan, K. / Maltseva, N. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The structure of a conserved protein domain (unknown function) from Corynebacterium diphtheriae. Authors: Tan, K. / Maltseva, N. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b4q.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b4q.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 3b4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/3b4q ftp://data.pdbj.org/pub/pdb/validation_reports/b4/3b4q | HTTPS FTP |
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-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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Details | Authors state that the biological unit is experimentally unknown, it is likely that chains A and B form a dimer. |
-Components
#1: Protein | Mass: 9958.781 Da / Num. of mol.: 2 / Fragment: Domain: Residues 117-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria) Species: Corynebacterium diphtheriae / Strain: NCTC 13129 / Biotype gravis / Gene: DIP0775 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6NIK0 #2: Chemical | ChemComp-SO4 / | #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: 2.25 Å3/Da / Density % sol: 45.42 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Li2SO4, 0.1M Tris-HCl, 30% PEG 3000, pH 8.5, 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: 0.97935 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→25.52 Å / Num. all: 25547 / Num. obs: 25547 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 38 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.4 / Num. unique all: 854 / % possible all: 65.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.55→25.52 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.286 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 22.984 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→25.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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