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Yorodumi- PDB-5tkw: 1.35 Angstrom Resolution Crystal Structure of a Pullulanase-speci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tkw | ||||||
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Title | 1.35 Angstrom Resolution Crystal Structure of a Pullulanase-specific Type II Secretion System Integral Cytoplasmic Membrane Protein GspL (N-terminal fragment; residues 1-237) from Klebsiella pneumoniae. | ||||||
Components | Type II secretion system protein LType II secretion system | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information Gram-negative-bacterium-type cell wall / protein secretion by the type II secretion system / type II protein secretion system complex Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 1.35 Angstrom Resolution Crystal Structure of a Pullulanase-specific Type II Secretion System Integral Cytoplasmic Membrane Protein GspL (N-terminal fragment; residues 1-237) from Klebsiella pneumoniae. Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tkw.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tkw.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 5tkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/5tkw ftp://data.pdbj.org/pub/pdb/validation_reports/tk/5tkw | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
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: 26533.602 Da / Num. of mol.: 1 / Fragment: UNP residues 8-244 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria) Gene: epsL, PMK1_02460 / Plasmid: pCPD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-magic / References: UniProt: A0A0C7KMJ7 |
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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: 1.98 Å3/Da / Density % sol: 37.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 8.9 mg/ml, 0.5M Sodium chloride, 0.1M Tris HCl (pH 8.3);Screen: Classics II (A5), 2.0M Ammonium sulfate, 0.1M HEPES (pH 7.5);Cryo: 2.0M Ammonium sulfate, 25% Sucrose. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2016 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. obs: 46935 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 45.9 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 2.03 / CC1/2: 0.629 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→29.75 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.887 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.055 / 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: 1.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.587 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→29.75 Å
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Refine LS restraints |
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