+Open data
-Basic information
Entry | Database: PDB / ID: 8pnj | ||||||
---|---|---|---|---|---|---|---|
Title | Chorismate mutase | ||||||
Components | chorismate mutase | ||||||
Keywords | UNKNOWN FUNCTION / chorismate mutase / cyclohexadienyl dehydratase / chorismate mutase/cyclohexadienyl dehydratase / cyclohexadienyl dehydratase/chorismate mutase / bifunctional chorismate mutase / bifunctional cyclohexadienyl dehydratase / bifunctional enzyme / shikimate pathway enzymes / metabolic enzymes / aromatic amino acid synthesis / protein crystal structure | ||||||
Function / homology | Function and homology information chorismate metabolic process / chorismate mutase / chorismate mutase activity Similarity search - Function | ||||||
Biological species | Aequoribacter fuscus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.355 Å | ||||||
Authors | Khatanbaatar, T. / Cordara, G. / Krengel, U. | ||||||
Funding support | Switzerland, 1items
| ||||||
Citation | Journal: To Be Published Title: Structural analysis of chorismate mutase and cyclohexadienyl dehydratase from Pseudomonas aeruginosa Authors: Khatanbaatar, T. / Cordara, G. / Krengel, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8pnj.cif.gz | 102 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8pnj.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 8pnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pnj_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8pnj_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8pnj_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 8pnj_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/8pnj ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pnj | HTTPS FTP |
-Related structure data
Related structure data | 8pniC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47854.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequoribacter fuscus (bacteria) / Gene: EYZ66_08225 / Production host: Escherichia coli (E. coli) / Strain (production host): KA29 / References: UniProt: A0A7Z2NRM1 |
---|
-Non-polymers , 5 types, 48 molecules
#2: Chemical | ChemComp-TSA / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.13 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1:1 volume ratio of 5 mg/ml protein in 20 mM TRIS-HCl, pH=8, 150 uM NaCl buffer and 0.1M BTP, pH=8.5 0.2M KSCN 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→46.336 Å / Num. obs: 20939 / % possible obs: 97.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 34.2 Å2 / CC1/2: 0.959 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.35→2.44 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1801 / CC1/2: 0.475 / % possible all: 85 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.355→46.336 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.876 / WRfactor Rfree: 0.284 / WRfactor Rwork: 0.215 / SU B: 9.888 / SU ML: 0.228 / Average fsc free: 0.9393 / Average fsc work: 0.9666 / Cross valid method: FREE R-VALUE / ESU R: 0.377 / ESU R Free: 0.283 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.122 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.355→46.336 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|