[English] 日本語
Yorodumi- PDB-7bvd: Anthranilate synthase component I (TrpE)[Mycolicibacterium smegmatis] -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bvd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Anthranilate synthase component I (TrpE)[Mycolicibacterium smegmatis] | |||||||||
Components | Anthranilate synthase component 1 | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Tryptophan biosynthesis pathway / Anthranilate synthasecomponent I / Mycolicibacterium smegmatis / MsTrpE | |||||||||
Function / homology | Function and homology information anthranilate synthase / anthranilate synthase activity / tryptophan biosynthetic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Chen, Y. / Che, S. / Zhang, Q. / Bartlam, M. | |||||||||
Funding support | China, 1items
| |||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Structure of subunit I of the anthranilate synthase complex of Mycolicibacterium smegmatis Authors: Chen, Y. / Jia, H. / Liu, R. / Che, S. / Zhang, Q. / Bartlam, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7bvd.cif.gz | 384.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7bvd.ent.gz | 309.7 KB | Display | PDB format |
PDBx/mmJSON format | 7bvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/7bvd ftp://data.pdbj.org/pub/pdb/validation_reports/bv/7bvd | HTTPS FTP |
---|
-Related structure data
Related structure data | 5cwaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 56372.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: trpE, ERS451418_03206 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0D6I7M8, UniProt: A0QX93*PLUS, anthranilate synthase |
---|
-Non-polymers , 5 types, 868 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PYR / | #5: Chemical | ChemComp-GOL / #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: 2.59 Å3/Da / Density % sol: 52.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M Magnesium formate dihydrate, 15% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 121727 / % possible obs: 97.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.05 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.04 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5900 / CC1/2: 0.91 / Rpim(I) all: 0.244 / % possible all: 94.4 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CWA Resolution: 1.7→38.49 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 35 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→38.49 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.76 Å
|