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- PDB-1amu: PHENYLALANINE ACTIVATING DOMAIN OF GRAMICIDIN SYNTHETASE 1 IN A C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1amu | ||||||
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Title | PHENYLALANINE ACTIVATING DOMAIN OF GRAMICIDIN SYNTHETASE 1 IN A COMPLEX WITH AMP AND PHENYLALANINE | ||||||
![]() | GRAMICIDIN SYNTHETASE 1 | ||||||
![]() | PEPTIDE SYNTHETASE / GRSA / ADENYLATE FORMING | ||||||
Function / homology | ![]() phenylalanine racemase (ATP-hydrolysing) / phenylalanine racemase (ATP-hydrolyzing) activity / ligase activity / antibiotic biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Conti, E. / Stachelhaus, T. / Marahiel, M.A. / Brick, P. | ||||||
![]() | ![]() Title: Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. Authors: Conti, E. / Stachelhaus, T. / Marahiel, M.A. / Brick, P. #1: ![]() Title: Modular Structure of Peptide Synthetases Revealed by Dissection of the Multifunctional Enzyme Grsa Authors: Stachelhaus, T. / Marahiel, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.3 KB | Display | ![]() |
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PDB format | ![]() | 176.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 43.5 KB | Display | |
Data in CIF | ![]() | 62.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 64131.793 Da / Num. of mol.: 2 Fragment: ADENYLATE FORMING DOMAIN, RESIDUES 1 - 556 PLUS A 7 RESIDUE C-TERMINAL TAG - SHHHHHH Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P14687, UniProt: P0C061*PLUS, phenylalanine racemase (ATP-hydrolysing) |
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-Non-polymers , 5 types, 577 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PHE.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PHE.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION TECHNIQUE. THE PROTEIN AT 15 MG/ML IN 10 MM TRIS-HCL PH7.8, 50 MM NACL, 15% GLYCEROL, 2 MM ATP, 2 MM L-PHE AND 4 MM MGCL2 WAS EQUILIBRATED WITH ...Details: CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION TECHNIQUE. THE PROTEIN AT 15 MG/ML IN 10 MM TRIS-HCL PH7.8, 50 MM NACL, 15% GLYCEROL, 2 MM ATP, 2 MM L-PHE AND 4 MM MGCL2 WAS EQUILIBRATED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 28-32%(W/V) METHOXY POLYETHYLENE GLYCOL 5000, 200 MM AMMONIUM SULFATE, AND 100 MM ADA PH6.5 AT 18C., vapor diffusion, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 9, 1996 |
Radiation | Monochromator: Y / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 91144 / % possible obs: 96.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 2.7 / % possible all: 88.3 |
Reflection | *PLUS Num. measured all: 230285 |
Reflection shell | *PLUS % possible obs: 88.3 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.99 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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