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- PDB-5gmu: Crystal structure of chorismate mutase like domain of bifunctiona... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gmu | ||||||
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Title | Crystal structure of chorismate mutase like domain of bifunctional DAHP synthase of Bacillus subtilis in complex with Chlorogenic acid | ||||||
![]() | Protein AroA(G) | ||||||
![]() | ISOMERASE / Type II chorismate mutase / CML domain / Bifunctional DAHP synthase / Chlorogenic acid | ||||||
Function / homology | ![]() chorismate mutase / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pratap, S. / Dev, A. / Sharma, V. / Yadav, R. / Narwal, M. / Tomar, S. / Kumar, P. | ||||||
![]() | ![]() Title: Structure of Chorismate Mutase-like Domain of DAHPS from Bacillus subtilis Complexed with Novel Inhibitor Reveals Conformational Plasticity of Active Site. Authors: Pratap, S. / Dev, A. / Kumar, V. / Yadav, R. / Narwal, M. / Tomar, S. / Kumar, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.5 KB | Display | ![]() |
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PDB format | ![]() | 68.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5go2C ![]() 3nvtS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 4 - 87 / Label seq-ID: 4 - 87
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Components
#1: Protein | Mass: 10430.755 Da / Num. of mol.: 2 Fragment: Chorismate Mutase type II like domain, UNP residues 1-90 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: aroA, BSU29750 Production host: ![]() ![]() Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P39912, chorismate mutase #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 2.0M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 16372 / % possible obs: 98 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.58 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 3.76 / CC1/2: 0.926 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NVT Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.897 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.143 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→50 Å
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Refine LS restraints |
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