[English] 日本語
Yorodumi- PDB-5ag8: CRYSTAL STRUCTURE OF A MUTANT (665I6H) OF THE C-TERMINAL DOMAIN O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ag8 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF A MUTANT (665I6H) OF THE C-TERMINAL DOMAIN OF RGPB | ||||||
Components | GINGIPAIN R2 | ||||||
Keywords | HYDROLASE / TYPE IX SECRETION SYSTEM | ||||||
Function / homology | Function and homology information gingipain R / calcium-dependent cysteine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | PORPHYROMONAS GINGIVALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Sci.Rep. / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ag8.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ag8.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ag8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ag8_validation.pdf.gz | 457.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ag8_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 5ag8_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 5ag8_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/5ag8 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/5ag8 | HTTPS FTP |
-Related structure data
Related structure data | 5ag9C 5hfsC 1cvrS 5agb C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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) PORPHYROMONAS GINGIVALIS (bacteria) / Strain: W83 / References: UniProt: P95493, gingipain R #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | HEXAHISTID | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % / Description: NONE |
---|---|
Crystal grow | Details: 30% PEG 4000, 0.2M (NH4)2SO4, 10% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|