- PDB-5tkw: 1.35 Angstrom Resolution Crystal Structure of a Pullulanase-speci... -
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Basic information
Entry
Database: PDB / ID: 5tkw
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 L
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
GspL cytoplasmic domain, C-terminal subdomain / Nucleotidyltransferase; domain 5 - #380 / Type II secretion system protein GspL / GspL, cytoplasmic actin-ATPase-like domain / GspL periplasmic domain / Type II secretion system (T2SS), protein L / GspL periplasmic domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
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
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0155
refinement
HKL-2000
datareduction
HKL-2000
datascaling
HKL-3000
phasing
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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.17629
2324
5 %
RANDOM
Rwork
0.14631
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obs
0.1478
44414
99.44 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.25 Å