[English] 日本語
Yorodumi- PDB-5e2l: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e2l | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis in complex with D-phenylalanine | |||||||||
Components | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase | |||||||||
Keywords | TRANSFERASE / 3-Deoxy-7-Phosphoheptulosonate Synthase / allosteric regulation / allosteric site / amino acid | |||||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / peptidoglycan-based cell wall / protein homooligomerization / manganese ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Reichau, S. / Jiao, W. / Parker, E.J. | |||||||||
Funding support | New Zealand, 2items
| |||||||||
Citation | Journal: Plos One / Year: 2016 Title: Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using -Amino Acids. Authors: Reichau, S. / Blackmore, N.J. / Jiao, W. / Parker, E.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5e2l.cif.gz | 357.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5e2l.ent.gz | 292.6 KB | Display | PDB format |
PDBx/mmJSON format | 5e2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e2l_validation.pdf.gz | 478.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5e2l_full_validation.pdf.gz | 486.8 KB | Display | |
Data in XML | 5e2l_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 5e2l_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/5e2l ftp://data.pdbj.org/pub/pdb/validation_reports/e2/5e2l | HTTPS FTP |
-Related structure data
Related structure data | 5e40C 5e4nC 5e5gC 5e7zC 3nv8S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 50828.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: aroG_1, ERS024751_03564, ERS094182_00944, ERS124362_02783 Production host: Escherichia coli (E. coli) References: UniProt: A0A0E8NFD1, UniProt: O53512*PLUS, 3-deoxy-7-phosphoheptulonate synthase |
---|
-Non-polymers , 6 types, 98 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.88 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M TRIS-HCl, pH 7.5, 1.5M ammonium sulfate, 12% v/v glycerol. Crystals were soaked in the same solution with an additional 10% v/v glycerol and 2.5 mM D-phenylalanine |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.97948 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 26, 2012 | |||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection twin |
| |||||||||||||||||||||||||||
Reflection | Resolution: 2.5→49 Å / Num. obs: 55365 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.059 / Net I/σ(I): 12 / Num. measured all: 620384 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3NV8 Resolution: 2.5→49 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.1462 / WRfactor Rwork: 0.131 / FOM work R set: 0.8967 / SU B: 7.197 / SU ML: 0.083 / SU R Cruickshank DPI: 0.0465 / SU Rfree: 0.0347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.035 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.88 Å2 / Biso mean: 35.628 Å2 / Biso min: 17.26 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→49 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|