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- PDB-5hl8: 1.93 Angstrom resolution crystal structure of a pullulanase-speci... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hl8 | ||||||
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Title | 1.93 Angstrom resolution crystal structure of a pullulanase-specific type II secretion system integral cytoplasmic membrane protein GspL (C-terminal fragment; residues 309-397) from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 | ||||||
![]() | Type II secretion system protein L | ||||||
![]() | PROTEIN TRANSPORT / pullulanase-specific type II secretion system / integral cytoplasmic membrane protein / structural genomics / CSGID / Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | General secretion pathway protein M, EpsM / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Halavaty, A.S. / Minasov, G. / Kiryukhina, O. / Grimshaw, S. / Light, S. / Dubrovska, I. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: 1.93 Angstrom resolution crystal structure of a pullulanase-specific type II secretion system integral cytoplasmic membrane protein GspL (C-terminal fragment; residues 309-397) from Klebsiella ...Title: 1.93 Angstrom resolution crystal structure of a pullulanase-specific type II secretion system integral cytoplasmic membrane protein GspL (C-terminal fragment; residues 309-397) from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 Authors: Halavaty, A.S. / Minasov, G. / Kiryukhina, O. / Grimshaw, S. / Light, S. / Dubrovska, I. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139 KB | Display | ![]() |
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PDB format | ![]() | 116.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.8 KB | Display | ![]() |
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Full document | ![]() | 455.4 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 10192.266 Da / Num. of mol.: 4 / Fragment: UNP residues 316-404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NTUH-K2044 / Gene: pulL, KpST82_0737 / Plasmid: pMCSG53 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: protein: 9.7 mg/mL 10 mM Tris-HCl pH 8.3 crystallization: The Classics II Suite conditions E7 (#55): 0.05 M MgCl2, 0.1 M HEPES pH 7.5, 30 % (v/v) PEG 550 MME cryo: crystallization conditions |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2015 / Details: C(111) |
Radiation | Monochromator: Be Lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→30 Å / Num. obs: 23407 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 58.1 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.834 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→26.44 Å
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Refine LS restraints |
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