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- PDB-5ag8: CRYSTAL STRUCTURE OF A MUTANT (665I6H) OF THE C-TERMINAL DOMAIN O... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ag8 | ||||||
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Title | CRYSTAL STRUCTURE OF A MUTANT (665I6H) OF THE C-TERMINAL DOMAIN OF RGPB | ||||||
![]() | GINGIPAIN R2 | ||||||
![]() | HYDROLASE / TYPE IX SECRETION SYSTEM | ||||||
Function / homology | ![]() gingipain R / calcium-dependent cysteine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | de Diego, I. / Ksiazek, M. / Mizgalska, D. / Golik, P. / Szmigielski, B. / Nowak, M. / Nowakowska, Z. / Potempa, B. / Koneru, L. / Nguyen, K.A. ...de Diego, I. / Ksiazek, M. / Mizgalska, D. / Golik, P. / Szmigielski, B. / Nowak, M. / Nowakowska, Z. / Potempa, B. / Koneru, L. / Nguyen, K.A. / Enghild, J. / Thogersen, I.B. / Dubin, G. / Gomis-Ruth, F.X. / Potempa, J. | ||||||
![]() | ![]() Title: The Outer-Membrane Export Signal of Porphyromonas Gingivalis Type Ix Secretion System (T9Ss) is a Conserved C-Terminal Beta-Sandwich Domain. Authors: De Diego, I. / Ksiazek, M. / Mizgalska, D. / Koneru, L. / Golik, P. / Szmigielski, B. / Nowak, M. / Nowakowska, Z. / Potempa, B. / Houston, J.A. / Enghild, J.J. / Thogersen, I.B. / Gao, J. / ...Authors: De Diego, I. / Ksiazek, M. / Mizgalska, D. / Koneru, L. / Golik, P. / Szmigielski, B. / Nowak, M. / Nowakowska, Z. / Potempa, B. / Houston, J.A. / Enghild, J.J. / Thogersen, I.B. / Gao, J. / Kwan, A.H. / Trewhella, J. / Dubin, G. / Gomis-Ruth, F.X. / Nguyen, K. / Potempa, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.7 KB | Display | ![]() |
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PDB format | ![]() | 99.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
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Full document | ![]() | 458.5 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ag9C ![]() 5hfsC ![]() 1cvrS ![]() 5agb 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17876.293 Da / Num. of mol.: 2 / Fragment: IGSF AND CTD DOMAINS, RESIDUES 577-736 / Source method: isolated from a natural source / Details: HEXAHISTIDINE INSERTION AFTER SER 664 / Source: (natural) ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | HEXAHISTID | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % / Description: NONE |
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Crystal grow | Details: 30% PEG 4000, 0.2M (NH4)2SO4, 10% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.92 Å / Num. obs: 23941 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.5 / % possible all: 91.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CVR Resolution: 1.9→48.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.574 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. RESIDUES 663-671 ARE DISORDERED
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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 mean: 24.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→48.92 Å
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Refine LS restraints |
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