[English] 日本語
Yorodumi- PDB-4jj9: Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jj9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase | ||||||
Components | 5-carboxymethyl-2-hydroxymuconate delta-isomerase | ||||||
Keywords | ISOMERASE / NYSGRC / PSI-Biology / Structural Genomics / New York Structural Genomics Research Consortium / alpha-beeta / trimer / homoprotocatechuate catabolic pathway | ||||||
Function / homology | Function and homology information 5-carboxymethyl-2-hydroxymuconate Delta-isomerase / 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity / : Similarity search - Function | ||||||
Biological species | Bordetella bronchiseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å | ||||||
Authors | Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Al Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4jj9.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4jj9.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jj9_validation.pdf.gz | 459.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4jj9_full_validation.pdf.gz | 463.8 KB | Display | |
Data in XML | 4jj9_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 4jj9_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/4jj9 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/4jj9 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18477.967 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: ATCC BAA-588 / NCTC 13252 / RB50 / Gene: BB0738, hpaF / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q7WPE6, UniProt: A0A0H3LHY8*PLUS, 5-carboxymethyl-2-hydroxymuconate Delta-isomerase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.37 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 0.2M Ammonium Sulfate, 0.1M Bis Tris, Glycerol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2013 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. all: 48870 / Num. obs: 48870 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.77→1.82 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.308 / Num. unique all: 3805 / % possible all: 94.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.248 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.069 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.764→1.81 Å / Total num. of bins used: 20
|