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- PDB-6iqs: Crystal structure of Prc with L245A and L340G mutations in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6iqs | ||||||
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Title | Crystal structure of Prc with L245A and L340G mutations in complex with NlpI | ||||||
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![]() | HYDROLASE / protein quality control / peptidoglycan remodeling | ||||||
Function / homology | ![]() C-terminal processing peptidase / peptidoglycan metabolic process / cell outer membrane / protein catabolic process / protein-macromolecule adaptor activity / outer membrane-bounded periplasmic space / endopeptidase activity / receptor-mediated virion attachment to host cell / cell cycle / cell division ...C-terminal processing peptidase / peptidoglycan metabolic process / cell outer membrane / protein catabolic process / protein-macromolecule adaptor activity / outer membrane-bounded periplasmic space / endopeptidase activity / receptor-mediated virion attachment to host cell / cell cycle / cell division / response to antibiotic / serine-type endopeptidase activity / signal transduction / protein homodimerization activity / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chuech, C.K. / Chang, C.I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for the Differential Regulatory Roles of the PDZ Domain in C-Terminal Processing Proteases. Authors: Chueh, C.K. / Som, N. / Ke, L.C. / Ho, M.R. / Reddy, M. / Chang, C.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 634.1 KB | Display | ![]() |
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PDB format | ![]() | 526 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.8 KB | Display | ![]() |
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Full document | ![]() | 488.7 KB | Display | |
Data in XML | ![]() | 53.1 KB | Display | |
Data in CIF | ![]() | 73.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6iqqC ![]() 6iqrC ![]() 6iquC ![]() 5wqlS S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 33841.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 77496.672 Da / Num. of mol.: 2 / Mutation: L245A/L340G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: prc, tsp, b1830, JW1819 / Production host: ![]() ![]() References: UniProt: P23865, C-terminal processing peptidase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 27, 2018 / Details: Cryo-cooled channel-cut Si(111) |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→30 Å / Num. obs: 69840 / % possible obs: 94.7 % / Redundancy: 5 % / Biso Wilson estimate: 41.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.042 / Rrim(I) all: 0.098 / Χ2: 0.919 / Net I/σ(I): 13.47 |
Reflection shell | Resolution: 2.69→2.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 3.684 / Num. unique obs: 6187 / CC1/2: 0.783 / Rpim(I) all: 0.394 / Rrim(I) all: 0.813 / Χ2: 0.773 / % possible all: 85.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WQL Resolution: 2.69→29.91 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 27.957 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.552 / ESU R Free: 0.305 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.34 Å2
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Refinement step | Cycle: 1 / Resolution: 2.69→29.91 Å
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Refine LS restraints |
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