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- PDB-4wvg: Crystal structure of the Type-I signal peptidase from Staphylococ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wvg | |||||||||
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Title | Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB). | |||||||||
![]() | Maltose-binding periplasmic protein,Signal peptidase IB | |||||||||
![]() | HYDROLASE / SpsB Type-I signal peptidase / Cell secretion / MBP fusion protein | |||||||||
Function / homology | ![]() signal peptidase I / thylakoid membrane organization / signal peptide processing / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Young, P.G. / Ting, Y.T. / Baker, E.N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Peptide binding to a bacterial signal peptidase visualized by peptide tethering and carrier-driven crystallization. Authors: Ting, Y.T. / Harris, P.W. / Batot, G. / Brimble, M.A. / Baker, E.N. / Young, P.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.2 KB | Display | ![]() |
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PDB format | ![]() | 92.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 831.9 KB | Display | ![]() |
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Full document | ![]() | 832.9 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wvhC ![]() 4wviC ![]() 4wvjC ![]() 1anfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 60301.949 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-393, UNP RESIDUES 26-191 / Mutation: S36A, R393N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12, Newman / Gene: malE, Z5632, ECs5017, spsB, SACOL0969 / Plasmid: pMBP-pProExHta / Details (production host): MBP fusion / Production host: ![]() ![]() References: UniProt: P0AEY0, UniProt: Q5HHB9, signal peptidase I |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Water | ChemComp-HOH / |
Sequence details | THIS MUTATION IS A RESULT OF PCR REACTION. THE MUTATION R393N HAS BEEN INTRODUCED TO STABILIZE THE ...THIS MUTATION IS A RESULT OF PCR REACTION. THE MUTATION R393N HAS BEEN INTRODUCED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.31 % / Description: Needles |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 12 % PEG 8000, 20 % ethylene glycol, 0.2 M amino acids mix (0.2 M sodium-L-glutamate, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine, 0.2 M DL-serine), 100 mM Tris.Cl pH 8.5 PH range: 8.0 - 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 25, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.05→19.44 Å / Num. obs: 36318 / % possible obs: 99.8 % / Redundancy: 7.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.082 / Net I/σ(I): 10.1 / Num. measured all: 275184 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ANF Resolution: 2.05→19.44 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.1901 / WRfactor Rwork: 0.1481 / FOM work R set: 0.7898 / SU B: 5.971 / SU ML: 0.151 / SU R Cruickshank DPI: 0.2001 / SU Rfree: 0.1796 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 64.54 Å2 / Biso mean: 29.325 Å2 / Biso min: 14.23 Å2
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Refinement step | Cycle: final / Resolution: 2.05→19.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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