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Open data
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Basic information
Entry | Database: PDB / ID: 1fr9 | ||||||
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Title | STRUCTURE OF E. COLI MOBA | ||||||
![]() | MOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS PROTEIN | ||||||
![]() | METAL BINDING PROTEIN / Molybdenum cofactor (Moco) / Moco Biosynthesis / Molybdopterin (MPT) / Molybdopterin Guanine Dinucleotide (MGD) | ||||||
Function / homology | ![]() molybdenum cofactor guanylyltransferase / molybdenum cofactor guanylyltransferase activity / bis(molybdopterin guanine dinucleotide)molybdenum biosynthetic process / nucleotidyltransferase activity / GTP binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lake, M.W. / Temple, C.A. / Rajagopalan, K.V. / Schindelin, H. | ||||||
![]() | ![]() Title: The crystal structure of the Escherichia coli MobA protein provides insight into molybdopterin guanine dinucleotide biosynthesis. Authors: Lake, M.W. / Temple, C.A. / Rajagopalan, K.V. / Schindelin, 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 | ![]() | 54.2 KB | Display | ![]() |
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PDB format | ![]() | 38.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.8 KB | Display | ![]() |
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Full document | ![]() | 445.1 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is an octamer constructed from chain A. The octamer has 42 symmetry and is entirely generated by crystallographic symmetry operations in the I422 tetragonal space group. His 49 from 2 different monomers along with 2 acetate ligands coordinate a zinc atom at the dimer interface. |
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Components
#1: Protein | Mass: 21669.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.65 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium acetate, cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.65→50 Å / Num. all: 58834 / Num. obs: 58834 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.4 | |||||||||||||||
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.411 / Num. unique all: 6007 / % possible all: 100 | |||||||||||||||
Reflection | *PLUS | |||||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Mean I/σ(I) obs: 1.2 |
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Processing
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Refinement | Resolution: 1.65→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Refmac dictionary / Details: Hydrogens have been added in the riding positions
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Solvent computation | Solvent model: Babinet's principle | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_chiral_restr / Dev ideal: 0.124 |