[English] 日本語

- PDB-9m1f: Crystal structure of E. coli tryptophanyl-tRNA synthetase complex... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 9m1f | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E. coli tryptophanyl-tRNA synthetase complexed with chuangxinmycin and ATP in closed-closed state | ||||||
![]() | Tryptophan--tRNA ligase | ||||||
![]() | LIGASE / tryptophanyl-tRNA synthetase / aminoacyl-tRNA synthetase / antibiotic | ||||||
Function / homology | ![]() tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ren, Y. / Wang, S. / Liu, W. / Fang, P. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Mechanistic insights into the ATP-mediated and species-dependent inhibition of TrpRS by chuangxinmycin. Authors: Ren, Y. / Wang, S. / Liu, W. / Wang, J. / Fang, P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 188.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 120.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 36.7 KB | Display | |
Data in CIF | ![]() | 51.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9kvcC ![]() 9kw0C ![]() 9kwhC ![]() 9kwwC ![]() 9kxbC ![]() 9kxrSC ![]() 9ky3C ![]() 9ky9C ![]() 9m1gC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38313.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_ ...Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_002885, C3F40_19370, CG704_07870, CIG67_21025, CTR35_001866, D9D43_04205, DD762_12005, DL968_00250, DNQ45_04190, DTL43_13995, DU321_12325, E4K51_10330, E6D34_04225, EIA08_11870, EPS97_04620, F7F11_12075, F7N46_14665, F9413_17445, F9461_03030, F9B07_12605, FGAF848_25410, FKO60_13960, FOI11_018845, FOI11_04335, FPS11_03390, FZU14_04195, G3V95_06005, G4A38_16925, G4A47_18515, G5603_11025, GAI89_06310, GNW61_08470, GOP25_12480, GP944_08250, GQE86_01825, GQN24_10725, HEP34_002452, HI055_002233, HJQ60_002846, HL563_11055, HL601_09110, HLX92_09755, HLZ50_06610, HMV95_07850, HVW04_17215, HVW43_18350, HVY77_01760, I6H00_19775, IH772_08800, J0541_002134, JNP96_25720, NCTC10764_03793, NCTC10974_00460, NCTC9044_01447, NCTC9073_00479, NCTC9077_00527, NCTC9706_02656, P6223_000209, Q2V20_09290, QDW62_01780, QO046_14075, R8G00_13645, SAMEA3472044_01080, SAMEA3472056_01981, SAMEA3752557_02035 Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 565 molecules 








#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|---|
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.75 % |
---|---|
Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979176 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→31.76 Å / Num. obs: 54988 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 16.56 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.92→1.97 Å / Rmerge(I) obs: 0.534 / Num. unique obs: 3749 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 9KXR Resolution: 1.92→30.45 Å / SU ML: 0.1995 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.6579 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→30.45 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|