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- PDB-3g5a: Crystal Structure of Candida glabrata FMN Adenylyltransferase in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g5a | ||||||
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Title | Crystal Structure of Candida glabrata FMN Adenylyltransferase in complex with FMN and ATP analog AMPCPP | ||||||
![]() | FMN adenylyltransferase | ||||||
![]() | TRANSFERASE / FMN binding / ATP binding / FAD biosynthesis / alpha/beta protein / Rossmann-like fold / extended loop region | ||||||
Function / homology | ![]() FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Huerta, C. / Zhang, H. | ||||||
![]() | ![]() Title: Structure and mechanism of a eukaryotic FMN adenylyltransferase. Authors: Huerta, C. / Borek, D. / Machius, M. / Grishin, N.V. / Zhang, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 419 KB | Display | ![]() |
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PDB format | ![]() | 338.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.3 MB | Display | ![]() |
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Full document | ![]() | 4.4 MB | Display | |
Data in XML | ![]() | 85.8 KB | Display | |
Data in CIF | ![]() | 122.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fwkSC ![]() 3g59C ![]() 3g6kC S: Starting model for refinement C: citing same article ( |
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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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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 35985.723 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1809 molecules ![](data/chem/img/APC.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-APC / #3: Chemical | ChemComp-FMN / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M Sodium acetate, pH 4.6, 8% (w/v) PEG 4000, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 13, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 123738 / Num. obs: 123738 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.088 / Χ2: 1.112 / Net I/σ(I): 11.517 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.094 / Num. unique all: 12367 / Rsym value: 0.447 / Χ2: 0.999 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FWK Resolution: 1.95→35.07 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.18 / SU B: 4.038 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.18 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.94 Å2 / Biso mean: 19.286 Å2 / Biso min: 4.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→35.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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