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- PDB-2phn: Crystal structure of an amide bond forming F420-gamma glutamyl li... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2phn | ||||||
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Title | Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus | ||||||
![]() | F420-0:gamma-glutamyl ligase | ||||||
![]() | LIGASE / gamma-glutamyl ligase / coenzyme F420 biosynthesis / amide bond forming enzyme / metal dependent / new fold / GDP binding / MCSG / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | ![]() coenzyme F420-0:L-glutamate ligase / coenzyme F420-1:gamma-L-glutamate ligase / coenzyme F420-0:L-glutamate ligase activity / coenzyme F420-1:gamma-L-glutamate ligase activity / F420-0 metabolic process / GTP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nocek, B. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Structure of an Amide Bond Forming F(420):gammagamma-glutamyl Ligase from Archaeoglobus Fulgidus - A Member of a New Family of Non-ribosomal Peptide Synthases. Authors: Nocek, B. / Evdokimova, E. / Proudfoot, M. / Kudritska, M. / Grochowski, L.L. / White, R.H. / Savchenko, A. / Yakunin, A.F. / Edwards, A. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT ASSEMBLY HAS BEEN CONFIRMED BY GEL FILTRATION. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.6 KB | Display | ![]() |
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PDB format | ![]() | 193.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 28.2 KB | Display | |
Data in CIF | ![]() | 42.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2g9iSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27762.896 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Species: Archaeoglobus fulgidus / Strain: DSM 4304, VC-16, JCM 9628, NBRC 100126 / Gene: cofE, AF_2256 / Plasmid: pET15b / Production host: ![]() ![]() References: UniProt: O28028, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Non-polymers , 6 types, 591 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.13 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate, 25% PEG 5000 MME, 10 mM GDP, MnCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2006 / Details: mirrors |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→40 Å / Num. all: 99727 / Num. obs: 99727 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.69 / Num. unique all: 4897 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2G9I Resolution: 1.35→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.678 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 15.446 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.386 Å / Total num. of bins used: 20
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